Starting phenix.real_space_refine on Mon Sep 23 17:54:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/09_2024/6u8y_20692.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/09_2024/6u8y_20692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/09_2024/6u8y_20692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/09_2024/6u8y_20692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/09_2024/6u8y_20692.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8y_20692/09_2024/6u8y_20692.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 258 5.16 5 C 32122 2.51 5 N 7704 2.21 5 O 8256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 357 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 48364 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1300 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 8, 'TRANS': 152} Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 685 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1792 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "H" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3696 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 468} Chain: "X" Number of atoms: 4677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4677 Classifications: {'peptide': 603} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 578} Chain breaks: 1 Chain: "J" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1461 Classifications: {'peptide': 177} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 161} Chain: "K" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1437 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "L" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3010 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 26, 'TRANS': 346} Chain: "M" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2319 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 15, 'TRANS': 285} Chain breaks: 1 Chain: "N" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1483 Classifications: {'peptide': 176} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 160} Chain breaks: 1 Chain: "a" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1300 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 8, 'TRANS': 152} Chain: "b" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "c" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "d" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 685 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "e" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1792 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain: "g" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "h" Number of atoms: 3696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3696 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 468} Chain: "x" Number of atoms: 4677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4677 Classifications: {'peptide': 603} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 578} Chain breaks: 1 Chain: "j" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1461 Classifications: {'peptide': 177} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 161} Chain: "k" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1437 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "l" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3010 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 26, 'TRANS': 346} Chain: "m" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2319 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 15, 'TRANS': 285} Chain breaks: 1 Chain: "n" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1483 Classifications: {'peptide': 176} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 160} Chain breaks: 1 Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15149 SG CYS J 93 104.344 149.602 40.032 1.00 28.91 S ATOM 15387 SG CYS J 123 111.604 149.957 39.313 1.00 18.86 S ATOM 23443 SG CYS N 102 116.187 156.410 27.846 1.00 48.79 S ATOM 39307 SG CYS j 93 97.452 58.254 39.938 1.00 28.82 S ATOM 39545 SG CYS j 123 89.981 57.823 39.317 1.00 21.53 S ATOM 47601 SG CYS n 102 85.582 51.570 28.419 1.00 48.79 S ATOM 47387 SG CYS n 71 89.949 52.838 28.959 1.00 31.06 S ATOM 47551 SG CYS n 96 88.453 51.410 34.789 1.00 48.79 S ATOM 47320 SG CYS n 61 82.620 41.855 23.688 1.00 30.43 S Time building chain proxies: 24.37, per 1000 atoms: 0.50 Number of scatterers: 48364 At special positions: 0 Unit cell: (202.713, 209.916, 131.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 258 16.00 O 8256 8.00 N 7704 7.00 C 32122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.33 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 J 201 " pdb="FE1 SF4 J 201 " - pdb=" SG CYS J 93 " pdb="FE2 SF4 J 201 " - pdb=" SG CYS J 123 " pdb="FE3 SF4 J 201 " - pdb=" SG CYS J 28 " pdb=" SF4 N 301 " pdb="FE1 SF4 N 301 " - pdb=" SG CYS N 102 " pdb="FE4 SF4 N 301 " - pdb=" SG CYS N 96 " pdb="FE2 SF4 N 301 " - pdb=" SG CYS N 99 " pdb="FE3 SF4 N 301 " - pdb=" SG CYS N 71 " pdb=" SF4 N 302 " pdb="FE4 SF4 N 302 " - pdb=" SG CYS N 67 " pdb="FE2 SF4 N 302 " - pdb=" SG CYS N 106 " pdb="FE3 SF4 N 302 " - pdb=" SG CYS N 64 " pdb="FE1 SF4 N 302 " - pdb=" SG CYS N 61 " pdb=" SF4 j 201 " pdb="FE2 SF4 j 201 " - pdb=" SG CYS j 123 " pdb="FE1 SF4 j 201 " - pdb=" SG CYS j 93 " pdb="FE3 SF4 j 201 " - pdb=" SG CYS j 28 " pdb=" SF4 n 301 " pdb="FE1 SF4 n 301 " - pdb=" SG CYS n 102 " pdb="FE4 SF4 n 301 " - pdb=" SG CYS n 96 " pdb="FE3 SF4 n 301 " - pdb=" SG CYS n 71 " pdb="FE2 SF4 n 301 " - pdb=" SG CYS n 99 " pdb=" SF4 n 302 " pdb="FE1 SF4 n 302 " - pdb=" SG CYS n 61 " pdb="FE4 SF4 n 302 " - pdb=" SG CYS n 67 " pdb="FE2 SF4 n 302 " - pdb=" SG CYS n 106 " pdb="FE3 SF4 n 302 " - pdb=" SG CYS n 64 " Number of angles added : 66 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11280 Finding SS restraints... Secondary structure from input PDB file: 265 helices and 24 sheets defined 59.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 7 through 25 removed outlier: 4.255A pdb=" N LEU A 11 " --> pdb=" O ILE A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.700A pdb=" N GLY A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.731A pdb=" N LEU A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'B' and resid 5 through 19 removed outlier: 3.989A pdb=" N LEU B 9 " --> pdb=" O ASN B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 29 through 54 removed outlier: 3.631A pdb=" N ILE B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 77 removed outlier: 4.485A pdb=" N PHE B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 28 removed outlier: 3.978A pdb=" N LEU C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 43 removed outlier: 3.502A pdb=" N ALA C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 58 removed outlier: 3.919A pdb=" N LEU C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 95 removed outlier: 3.865A pdb=" N THR C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Proline residue: C 83 - end of helix removed outlier: 3.597A pdb=" N ALA C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS C 95 " --> pdb=" O ARG C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.933A pdb=" N LYS C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 21 Processing helix chain 'D' and resid 27 through 49 Processing helix chain 'D' and resid 51 through 63 removed outlier: 3.658A pdb=" N ALA D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'E' and resid 5 through 25 Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.711A pdb=" N TYR E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 61 removed outlier: 3.835A pdb=" N VAL E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 85 Processing helix chain 'E' and resid 102 through 123 removed outlier: 3.541A pdb=" N LEU E 109 " --> pdb=" O GLY E 105 " (cutoff:3.500A) Proline residue: E 111 - end of helix removed outlier: 3.730A pdb=" N PHE E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE E 121 " --> pdb=" O GLY E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 147 removed outlier: 4.331A pdb=" N GLY E 134 " --> pdb=" O GLY E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 176 removed outlier: 3.793A pdb=" N GLU E 163 " --> pdb=" O PHE E 159 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR E 173 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 Processing helix chain 'E' and resid 202 through 206 removed outlier: 4.163A pdb=" N SER E 205 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY E 206 " --> pdb=" O LEU E 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 202 through 206' Processing helix chain 'E' and resid 208 through 232 removed outlier: 3.872A pdb=" N ILE E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER E 225 " --> pdb=" O GLY E 221 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY E 226 " --> pdb=" O THR E 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 22 removed outlier: 3.810A pdb=" N VAL G 20 " --> pdb=" O GLY G 16 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL G 22 " --> pdb=" O TYR G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 46 Processing helix chain 'G' and resid 71 through 80 removed outlier: 3.563A pdb=" N LEU G 77 " --> pdb=" O GLN G 73 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 101 removed outlier: 3.687A pdb=" N SER G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 93 " --> pdb=" O MET G 89 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 5 removed outlier: 3.536A pdb=" N ALA H 5 " --> pdb=" O SER H 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2 through 5' Processing helix chain 'H' and resid 6 through 19 removed outlier: 3.924A pdb=" N ALA H 10 " --> pdb=" O ALA H 6 " (cutoff:3.500A) Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 31 through 53 removed outlier: 3.947A pdb=" N VAL H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE H 36 " --> pdb=" O PRO H 32 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE H 37 " --> pdb=" O PHE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 96 removed outlier: 3.894A pdb=" N LEU H 82 " --> pdb=" O HIS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 125 removed outlier: 3.831A pdb=" N LEU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 148 Processing helix chain 'H' and resid 156 through 185 removed outlier: 3.764A pdb=" N SER H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 162 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 195 removed outlier: 4.040A pdb=" N MET H 195 " --> pdb=" O ALA H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 220 removed outlier: 4.525A pdb=" N GLU H 219 " --> pdb=" O GLY H 215 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA H 220 " --> pdb=" O LEU H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 233 Processing helix chain 'H' and resid 237 through 247 removed outlier: 3.828A pdb=" N VAL H 242 " --> pdb=" O HIS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.760A pdb=" N TYR H 261 " --> pdb=" O ALA H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 291 removed outlier: 3.599A pdb=" N ALA H 278 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA H 287 " --> pdb=" O THR H 283 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU H 288 " --> pdb=" O VAL H 284 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA H 291 " --> pdb=" O ALA H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 317 removed outlier: 4.091A pdb=" N SER H 304 " --> pdb=" O MET H 300 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE H 306 " --> pdb=" O ALA H 302 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 309 " --> pdb=" O SER H 305 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU H 311 " --> pdb=" O GLY H 307 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER H 317 " --> pdb=" O ALA H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 352 removed outlier: 3.941A pdb=" N ASN H 333 " --> pdb=" O PHE H 329 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 335 " --> pdb=" O MET H 331 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE H 336 " --> pdb=" O LEU H 332 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE H 342 " --> pdb=" O LYS H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 360 Processing helix chain 'H' and resid 369 through 383 removed outlier: 3.800A pdb=" N ALA H 380 " --> pdb=" O ILE H 376 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR H 381 " --> pdb=" O GLY H 377 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL H 382 " --> pdb=" O GLY H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 400 removed outlier: 3.647A pdb=" N TRP H 391 " --> pdb=" O PHE H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 420 removed outlier: 3.906A pdb=" N VAL H 417 " --> pdb=" O LEU H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 425 removed outlier: 3.881A pdb=" N PHE H 424 " --> pdb=" O ALA H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 432 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 463 through 473 removed outlier: 3.748A pdb=" N ASN H 468 " --> pdb=" O THR H 464 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU H 469 " --> pdb=" O PRO H 465 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 470 " --> pdb=" O PHE H 466 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR H 471 " --> pdb=" O TRP H 467 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS H 472 " --> pdb=" O ASN H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 486 Processing helix chain 'X' and resid 5 through 18 Proline residue: X 11 - end of helix Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 36 through 45 removed outlier: 4.096A pdb=" N TYR X 40 " --> pdb=" O ALA X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 50 removed outlier: 3.717A pdb=" N GLU X 50 " --> pdb=" O PRO X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 89 Processing helix chain 'X' and resid 100 through 105 removed outlier: 3.597A pdb=" N LEU X 105 " --> pdb=" O TRP X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 116 Processing helix chain 'X' and resid 122 through 139 Processing helix chain 'X' and resid 142 through 170 removed outlier: 3.590A pdb=" N LYS X 148 " --> pdb=" O HIS X 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR X 149 " --> pdb=" O ALA X 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 186 Processing helix chain 'X' and resid 203 through 214 removed outlier: 3.603A pdb=" N ALA X 208 " --> pdb=" O LEU X 204 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 231 Processing helix chain 'X' and resid 235 through 245 removed outlier: 4.028A pdb=" N ALA X 240 " --> pdb=" O GLN X 236 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N MET X 241 " --> pdb=" O SER X 237 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE X 242 " --> pdb=" O TYR X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 247 through 261 removed outlier: 3.906A pdb=" N VAL X 251 " --> pdb=" O SER X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 268 removed outlier: 3.740A pdb=" N THR X 268 " --> pdb=" O LYS X 264 " (cutoff:3.500A) Processing helix chain 'X' and resid 276 through 297 Processing helix chain 'X' and resid 304 through 312 removed outlier: 3.889A pdb=" N TYR X 309 " --> pdb=" O LYS X 305 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 322 removed outlier: 3.728A pdb=" N ILE X 318 " --> pdb=" O GLN X 314 " (cutoff:3.500A) Processing helix chain 'X' and resid 328 through 357 removed outlier: 4.298A pdb=" N TYR X 335 " --> pdb=" O ALA X 331 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU X 346 " --> pdb=" O LEU X 342 " (cutoff:3.500A) Processing helix chain 'X' and resid 373 through 386 Processing helix chain 'X' and resid 393 through 408 removed outlier: 3.769A pdb=" N ALA X 397 " --> pdb=" O MET X 393 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE X 407 " --> pdb=" O PHE X 403 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER X 408 " --> pdb=" O GLU X 404 " (cutoff:3.500A) Processing helix chain 'X' and resid 411 through 433 removed outlier: 3.644A pdb=" N ALA X 416 " --> pdb=" O PRO X 412 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET X 417 " --> pdb=" O ILE X 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL X 418 " --> pdb=" O LEU X 414 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR X 428 " --> pdb=" O ILE X 424 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU X 429 " --> pdb=" O GLY X 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE X 430 " --> pdb=" O PHE X 426 " (cutoff:3.500A) Processing helix chain 'X' and resid 452 through 471 removed outlier: 3.767A pdb=" N GLY X 458 " --> pdb=" O PRO X 454 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL X 471 " --> pdb=" O VAL X 467 " (cutoff:3.500A) Processing helix chain 'X' and resid 474 through 482 removed outlier: 3.521A pdb=" N LYS X 482 " --> pdb=" O ARG X 478 " (cutoff:3.500A) Processing helix chain 'X' and resid 505 through 522 removed outlier: 4.827A pdb=" N TRP X 511 " --> pdb=" O LEU X 507 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU X 512 " --> pdb=" O LEU X 508 " (cutoff:3.500A) Processing helix chain 'X' and resid 557 through 564 removed outlier: 3.747A pdb=" N MET X 564 " --> pdb=" O LEU X 560 " (cutoff:3.500A) Processing helix chain 'X' and resid 566 through 570 removed outlier: 3.793A pdb=" N MET X 570 " --> pdb=" O TRP X 567 " (cutoff:3.500A) Processing helix chain 'X' and resid 572 through 594 removed outlier: 3.717A pdb=" N SER X 592 " --> pdb=" O ASP X 588 " (cutoff:3.500A) Processing helix chain 'X' and resid 598 through 616 removed outlier: 3.682A pdb=" N TYR X 602 " --> pdb=" O ASN X 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 16 removed outlier: 3.510A pdb=" N TRP J 13 " --> pdb=" O PRO J 9 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS J 16 " --> pdb=" O ASN J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 38 removed outlier: 4.023A pdb=" N THR J 38 " --> pdb=" O PRO J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 47 Processing helix chain 'J' and resid 67 through 79 removed outlier: 3.799A pdb=" N LYS J 72 " --> pdb=" O PRO J 68 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG J 73 " --> pdb=" O LYS J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 103 removed outlier: 4.398A pdb=" N ASP J 102 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA J 103 " --> pdb=" O TYR J 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 99 through 103' Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 126 through 144 removed outlier: 4.406A pdb=" N ASN J 143 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 removed outlier: 4.290A pdb=" N GLU J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 167 removed outlier: 4.006A pdb=" N TYR J 159 " --> pdb=" O ASN J 155 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS J 161 " --> pdb=" O GLU J 157 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU J 166 " --> pdb=" O ASN J 162 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU J 167 " --> pdb=" O GLN J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 175 Processing helix chain 'K' and resid 5 through 16 removed outlier: 3.873A pdb=" N LYS K 16 " --> pdb=" O GLN K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 39 removed outlier: 3.784A pdb=" N LYS K 38 " --> pdb=" O PRO K 35 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE K 39 " --> pdb=" O ALA K 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 35 through 39' Processing helix chain 'K' and resid 42 through 50 removed outlier: 3.788A pdb=" N ASN K 50 " --> pdb=" O MET K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 109 removed outlier: 3.561A pdb=" N GLU K 109 " --> pdb=" O PRO K 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 106 through 109' Processing helix chain 'K' and resid 110 through 119 removed outlier: 3.588A pdb=" N PHE K 119 " --> pdb=" O VAL K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 159 Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.706A pdb=" N ILE L 84 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'L' and resid 90 through 105 removed outlier: 3.647A pdb=" N TYR L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP L 101 " --> pdb=" O SER L 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU L 102 " --> pdb=" O MET L 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE L 104 " --> pdb=" O VAL L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 137 removed outlier: 3.711A pdb=" N ARG L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 163 removed outlier: 3.547A pdb=" N ALA L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG L 154 " --> pdb=" O ALA L 150 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE L 155 " --> pdb=" O TYR L 151 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN L 161 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 201 removed outlier: 3.957A pdb=" N GLN L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG L 191 " --> pdb=" O LEU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 209 Processing helix chain 'L' and resid 213 through 218 Processing helix chain 'L' and resid 247 through 252 Processing helix chain 'L' and resid 273 through 297 removed outlier: 4.587A pdb=" N ARG L 279 " --> pdb=" O ARG L 275 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP L 295 " --> pdb=" O GLU L 291 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET L 296 " --> pdb=" O GLN L 292 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY L 297 " --> pdb=" O LEU L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 311 removed outlier: 3.753A pdb=" N LEU L 310 " --> pdb=" O ASP L 307 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS L 311 " --> pdb=" O PRO L 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 307 through 311' Processing helix chain 'L' and resid 371 through 374 Processing helix chain 'L' and resid 375 through 382 Processing helix chain 'L' and resid 385 through 389 removed outlier: 3.672A pdb=" N ILE L 389 " --> pdb=" O PRO L 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 33 removed outlier: 4.815A pdb=" N ILE M 21 " --> pdb=" O PHE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 52 removed outlier: 4.133A pdb=" N ILE M 46 " --> pdb=" O TYR M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 80 removed outlier: 3.845A pdb=" N ASP M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE M 66 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE M 68 " --> pdb=" O TYR M 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 105 removed outlier: 3.928A pdb=" N GLU M 104 " --> pdb=" O THR M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 113 removed outlier: 4.258A pdb=" N MET M 111 " --> pdb=" O MET M 107 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA M 113 " --> pdb=" O GLY M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 136 removed outlier: 3.852A pdb=" N LEU M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR M 132 " --> pdb=" O ARG M 128 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU M 133 " --> pdb=" O ALA M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 152 removed outlier: 3.908A pdb=" N LEU M 142 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR M 150 " --> pdb=" O ALA M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 166 removed outlier: 4.427A pdb=" N ALA M 162 " --> pdb=" O GLU M 158 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 191 removed outlier: 3.552A pdb=" N LEU M 176 " --> pdb=" O HIS M 172 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA M 178 " --> pdb=" O PRO M 174 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN M 187 " --> pdb=" O ASP M 183 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA M 188 " --> pdb=" O ILE M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 196 removed outlier: 3.557A pdb=" N ASP M 196 " --> pdb=" O GLU M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 210 removed outlier: 3.739A pdb=" N MET M 209 " --> pdb=" O LEU M 206 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL M 210 " --> pdb=" O GLY M 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 206 through 210' Processing helix chain 'M' and resid 213 through 240 removed outlier: 3.511A pdb=" N ILE M 238 " --> pdb=" O PHE M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 277 removed outlier: 3.975A pdb=" N ALA M 257 " --> pdb=" O LEU M 253 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL M 269 " --> pdb=" O LYS M 265 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE M 275 " --> pdb=" O LEU M 271 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL M 276 " --> pdb=" O ILE M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 307 removed outlier: 3.692A pdb=" N TYR M 292 " --> pdb=" O ALA M 288 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TRP M 293 " --> pdb=" O ALA M 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS M 294 " --> pdb=" O LYS M 290 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP M 295 " --> pdb=" O PHE M 291 " (cutoff:3.500A) Proline residue: M 296 - end of helix Processing helix chain 'N' and resid 21 through 31 removed outlier: 4.069A pdb=" N LYS N 28 " --> pdb=" O PHE N 25 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR N 29 " --> pdb=" O GLY N 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU N 30 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE N 31 " --> pdb=" O LYS N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 70 removed outlier: 3.641A pdb=" N GLN N 69 " --> pdb=" O MET N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 132 removed outlier: 3.979A pdb=" N LEU N 129 " --> pdb=" O GLU N 126 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU N 130 " --> pdb=" O GLU N 127 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR N 131 " --> pdb=" O LEU N 128 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP N 132 " --> pdb=" O LEU N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 144 Processing helix chain 'a' and resid 8 through 25 Processing helix chain 'a' and resid 32 through 47 removed outlier: 3.698A pdb=" N GLY a 36 " --> pdb=" O GLU a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 70 removed outlier: 3.731A pdb=" N LEU a 65 " --> pdb=" O PRO a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 88 Processing helix chain 'a' and resid 110 through 122 Processing helix chain 'a' and resid 159 through 164 Processing helix chain 'b' and resid 5 through 19 removed outlier: 3.989A pdb=" N LEU b 9 " --> pdb=" O ASN b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 24 Processing helix chain 'b' and resid 29 through 54 removed outlier: 3.630A pdb=" N ILE b 37 " --> pdb=" O VAL b 33 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR b 40 " --> pdb=" O ASP b 36 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU b 48 " --> pdb=" O GLY b 44 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA b 50 " --> pdb=" O MET b 46 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU b 51 " --> pdb=" O VAL b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 77 removed outlier: 4.485A pdb=" N PHE b 70 " --> pdb=" O ALA b 66 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY b 72 " --> pdb=" O LEU b 68 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 28 removed outlier: 3.979A pdb=" N LEU c 13 " --> pdb=" O GLU c 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE c 27 " --> pdb=" O THR c 23 " (cutoff:3.500A) Processing helix chain 'c' and resid 31 through 43 removed outlier: 3.502A pdb=" N ALA c 39 " --> pdb=" O ARG c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 58 removed outlier: 3.919A pdb=" N LEU c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 65 through 95 removed outlier: 3.865A pdb=" N THR c 69 " --> pdb=" O VAL c 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS c 70 " --> pdb=" O ALA c 66 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU c 80 " --> pdb=" O ALA c 76 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN c 82 " --> pdb=" O LEU c 78 " (cutoff:3.500A) Proline residue: c 83 - end of helix removed outlier: 3.597A pdb=" N ALA c 92 " --> pdb=" O ALA c 88 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS c 95 " --> pdb=" O ARG c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 114 removed outlier: 3.933A pdb=" N LYS c 110 " --> pdb=" O VAL c 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 21 Processing helix chain 'd' and resid 27 through 49 Processing helix chain 'd' and resid 51 through 63 removed outlier: 3.658A pdb=" N ALA d 63 " --> pdb=" O ALA d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 75 Processing helix chain 'e' and resid 5 through 24 Processing helix chain 'e' and resid 37 through 44 removed outlier: 3.712A pdb=" N TYR e 41 " --> pdb=" O VAL e 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU e 42 " --> pdb=" O GLY e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 61 removed outlier: 3.834A pdb=" N VAL e 60 " --> pdb=" O THR e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 66 through 85 Processing helix chain 'e' and resid 102 through 123 removed outlier: 3.541A pdb=" N LEU e 109 " --> pdb=" O GLY e 105 " (cutoff:3.500A) Proline residue: e 111 - end of helix removed outlier: 3.729A pdb=" N PHE e 116 " --> pdb=" O PHE e 112 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE e 121 " --> pdb=" O GLY e 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 147 removed outlier: 4.332A pdb=" N GLY e 134 " --> pdb=" O GLY e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 176 removed outlier: 3.792A pdb=" N GLU e 163 " --> pdb=" O PHE e 159 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR e 173 " --> pdb=" O GLY e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 180 Processing helix chain 'e' and resid 208 through 232 removed outlier: 3.872A pdb=" N ILE e 212 " --> pdb=" O PHE e 208 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU e 224 " --> pdb=" O VAL e 220 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER e 225 " --> pdb=" O GLY e 221 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY e 226 " --> pdb=" O THR e 222 " (cutoff:3.500A) Processing helix chain 'g' and resid 3 through 22 removed outlier: 3.810A pdb=" N VAL g 20 " --> pdb=" O GLY g 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU g 21 " --> pdb=" O LEU g 17 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL g 22 " --> pdb=" O TYR g 18 " (cutoff:3.500A) Processing helix chain 'g' and resid 25 through 46 Processing helix chain 'g' and resid 71 through 80 removed outlier: 3.563A pdb=" N LEU g 77 " --> pdb=" O GLN g 73 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR g 78 " --> pdb=" O ALA g 74 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA g 79 " --> pdb=" O LEU g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 101 removed outlier: 3.687A pdb=" N SER g 92 " --> pdb=" O ALA g 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL g 93 " --> pdb=" O MET g 89 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR g 98 " --> pdb=" O ALA g 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 5 removed outlier: 3.536A pdb=" N ALA h 5 " --> pdb=" O SER h 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 2 through 5' Processing helix chain 'h' and resid 6 through 19 removed outlier: 3.924A pdb=" N ALA h 10 " --> pdb=" O ALA h 6 " (cutoff:3.500A) Proline residue: h 12 - end of helix Processing helix chain 'h' and resid 31 through 53 removed outlier: 3.947A pdb=" N VAL h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE h 36 " --> pdb=" O PRO h 32 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE h 37 " --> pdb=" O PHE h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 96 removed outlier: 3.895A pdb=" N LEU h 82 " --> pdb=" O HIS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 109 through 125 removed outlier: 3.831A pdb=" N LEU h 113 " --> pdb=" O LYS h 109 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 148 Processing helix chain 'h' and resid 156 through 185 removed outlier: 3.765A pdb=" N SER h 160 " --> pdb=" O ALA h 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET h 161 " --> pdb=" O ALA h 157 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS h 162 " --> pdb=" O GLU h 158 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR h 163 " --> pdb=" O ALA h 159 " (cutoff:3.500A) Processing helix chain 'h' and resid 189 through 195 removed outlier: 4.040A pdb=" N MET h 195 " --> pdb=" O ALA h 191 " (cutoff:3.500A) Processing helix chain 'h' and resid 204 through 220 removed outlier: 4.524A pdb=" N GLU h 219 " --> pdb=" O GLY h 215 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA h 220 " --> pdb=" O LEU h 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 228 through 233 Processing helix chain 'h' and resid 237 through 247 removed outlier: 3.828A pdb=" N VAL h 242 " --> pdb=" O HIS h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 247 through 261 removed outlier: 3.760A pdb=" N TYR h 261 " --> pdb=" O ALA h 257 " (cutoff:3.500A) Processing helix chain 'h' and resid 268 through 291 removed outlier: 3.600A pdb=" N ALA h 278 " --> pdb=" O LYS h 274 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE h 286 " --> pdb=" O LEU h 282 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA h 287 " --> pdb=" O THR h 283 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU h 288 " --> pdb=" O VAL h 284 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA h 291 " --> pdb=" O ALA h 287 " (cutoff:3.500A) Processing helix chain 'h' and resid 296 through 317 removed outlier: 4.091A pdb=" N SER h 304 " --> pdb=" O MET h 300 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE h 306 " --> pdb=" O ALA h 302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL h 309 " --> pdb=" O SER h 305 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU h 311 " --> pdb=" O GLY h 307 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA h 315 " --> pdb=" O LEU h 311 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER h 317 " --> pdb=" O ALA h 313 " (cutoff:3.500A) Processing helix chain 'h' and resid 327 through 352 removed outlier: 3.941A pdb=" N ASN h 333 " --> pdb=" O PHE h 329 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA h 335 " --> pdb=" O MET h 331 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE h 336 " --> pdb=" O LEU h 332 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE h 342 " --> pdb=" O LYS h 338 " (cutoff:3.500A) Processing helix chain 'h' and resid 356 through 360 Processing helix chain 'h' and resid 369 through 383 removed outlier: 3.800A pdb=" N ALA h 380 " --> pdb=" O ILE h 376 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR h 381 " --> pdb=" O GLY h 377 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL h 382 " --> pdb=" O GLY h 378 " (cutoff:3.500A) Processing helix chain 'h' and resid 387 through 400 removed outlier: 3.647A pdb=" N TRP h 391 " --> pdb=" O PHE h 387 " (cutoff:3.500A) Processing helix chain 'h' and resid 411 through 420 removed outlier: 3.905A pdb=" N VAL h 417 " --> pdb=" O LEU h 413 " (cutoff:3.500A) Processing helix chain 'h' and resid 420 through 425 removed outlier: 3.882A pdb=" N PHE h 424 " --> pdb=" O ALA h 420 " (cutoff:3.500A) Processing helix chain 'h' and resid 427 through 432 Processing helix chain 'h' and resid 447 through 454 Processing helix chain 'h' and resid 463 through 473 removed outlier: 3.747A pdb=" N ASN h 468 " --> pdb=" O THR h 464 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU h 469 " --> pdb=" O PRO h 465 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL h 470 " --> pdb=" O PHE h 466 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR h 471 " --> pdb=" O TRP h 467 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS h 472 " --> pdb=" O ASN h 468 " (cutoff:3.500A) Processing helix chain 'h' and resid 480 through 486 Processing helix chain 'x' and resid 5 through 18 Proline residue: x 11 - end of helix Processing helix chain 'x' and resid 28 through 33 Processing helix chain 'x' and resid 36 through 45 removed outlier: 4.096A pdb=" N TYR x 40 " --> pdb=" O ALA x 36 " (cutoff:3.500A) Processing helix chain 'x' and resid 46 through 50 removed outlier: 3.717A pdb=" N GLU x 50 " --> pdb=" O PRO x 47 " (cutoff:3.500A) Processing helix chain 'x' and resid 72 through 89 Processing helix chain 'x' and resid 100 through 105 removed outlier: 3.598A pdb=" N LEU x 105 " --> pdb=" O TRP x 101 " (cutoff:3.500A) Processing helix chain 'x' and resid 105 through 116 Processing helix chain 'x' and resid 122 through 139 Processing helix chain 'x' and resid 142 through 170 removed outlier: 3.589A pdb=" N LYS x 148 " --> pdb=" O HIS x 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR x 149 " --> pdb=" O ALA x 145 " (cutoff:3.500A) Processing helix chain 'x' and resid 178 through 186 Processing helix chain 'x' and resid 203 through 214 removed outlier: 3.603A pdb=" N ALA x 208 " --> pdb=" O LEU x 204 " (cutoff:3.500A) Processing helix chain 'x' and resid 226 through 231 Processing helix chain 'x' and resid 235 through 245 removed outlier: 4.028A pdb=" N ALA x 240 " --> pdb=" O GLN x 236 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N MET x 241 " --> pdb=" O SER x 237 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE x 242 " --> pdb=" O TYR x 238 " (cutoff:3.500A) Processing helix chain 'x' and resid 247 through 261 removed outlier: 3.905A pdb=" N VAL x 251 " --> pdb=" O SER x 247 " (cutoff:3.500A) Processing helix chain 'x' and resid 263 through 268 removed outlier: 3.741A pdb=" N THR x 268 " --> pdb=" O LYS x 264 " (cutoff:3.500A) Processing helix chain 'x' and resid 276 through 297 Processing helix chain 'x' and resid 304 through 312 removed outlier: 3.890A pdb=" N TYR x 309 " --> pdb=" O LYS x 305 " (cutoff:3.500A) Processing helix chain 'x' and resid 314 through 322 removed outlier: 3.728A pdb=" N ILE x 318 " --> pdb=" O GLN x 314 " (cutoff:3.500A) Processing helix chain 'x' and resid 328 through 357 removed outlier: 4.298A pdb=" N TYR x 335 " --> pdb=" O ALA x 331 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU x 346 " --> pdb=" O LEU x 342 " (cutoff:3.500A) Processing helix chain 'x' and resid 373 through 386 Processing helix chain 'x' and resid 393 through 408 removed outlier: 3.768A pdb=" N ALA x 397 " --> pdb=" O MET x 393 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE x 407 " --> pdb=" O PHE x 403 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER x 408 " --> pdb=" O GLU x 404 " (cutoff:3.500A) Processing helix chain 'x' and resid 411 through 433 removed outlier: 3.644A pdb=" N ALA x 416 " --> pdb=" O PRO x 412 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET x 417 " --> pdb=" O ILE x 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL x 418 " --> pdb=" O LEU x 414 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR x 428 " --> pdb=" O ILE x 424 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU x 429 " --> pdb=" O GLY x 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE x 430 " --> pdb=" O PHE x 426 " (cutoff:3.500A) Processing helix chain 'x' and resid 452 through 471 removed outlier: 3.767A pdb=" N GLY x 458 " --> pdb=" O PRO x 454 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL x 471 " --> pdb=" O VAL x 467 " (cutoff:3.500A) Processing helix chain 'x' and resid 474 through 482 removed outlier: 3.520A pdb=" N LYS x 482 " --> pdb=" O ARG x 478 " (cutoff:3.500A) Processing helix chain 'x' and resid 505 through 522 removed outlier: 4.828A pdb=" N TRP x 511 " --> pdb=" O LEU x 507 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU x 512 " --> pdb=" O LEU x 508 " (cutoff:3.500A) Processing helix chain 'x' and resid 557 through 564 removed outlier: 3.748A pdb=" N MET x 564 " --> pdb=" O LEU x 560 " (cutoff:3.500A) Processing helix chain 'x' and resid 566 through 570 removed outlier: 3.792A pdb=" N MET x 570 " --> pdb=" O TRP x 567 " (cutoff:3.500A) Processing helix chain 'x' and resid 572 through 594 removed outlier: 3.716A pdb=" N SER x 592 " --> pdb=" O ASP x 588 " (cutoff:3.500A) Processing helix chain 'x' and resid 598 through 616 removed outlier: 3.682A pdb=" N TYR x 602 " --> pdb=" O ASN x 598 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 16 removed outlier: 3.510A pdb=" N TRP j 13 " --> pdb=" O PRO j 9 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA j 14 " --> pdb=" O LEU j 10 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS j 16 " --> pdb=" O ASN j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 34 through 38 removed outlier: 4.023A pdb=" N THR j 38 " --> pdb=" O PRO j 35 " (cutoff:3.500A) Processing helix chain 'j' and resid 43 through 47 Processing helix chain 'j' and resid 67 through 79 removed outlier: 3.800A pdb=" N LYS j 72 " --> pdb=" O PRO j 68 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG j 73 " --> pdb=" O LYS j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 99 through 103 removed outlier: 4.399A pdb=" N ASP j 102 " --> pdb=" O ILE j 99 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA j 103 " --> pdb=" O TYR j 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 99 through 103' Processing helix chain 'j' and resid 109 through 113 Processing helix chain 'j' and resid 126 through 144 removed outlier: 4.406A pdb=" N ASN j 143 " --> pdb=" O GLU j 139 " (cutoff:3.500A) Processing helix chain 'j' and resid 150 through 155 removed outlier: 4.290A pdb=" N GLU j 154 " --> pdb=" O LYS j 150 " (cutoff:3.500A) Processing helix chain 'j' and resid 155 through 167 removed outlier: 4.006A pdb=" N TYR j 159 " --> pdb=" O ASN j 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS j 161 " --> pdb=" O GLU j 157 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU j 166 " --> pdb=" O ASN j 162 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU j 167 " --> pdb=" O GLN j 163 " (cutoff:3.500A) Processing helix chain 'j' and resid 170 through 175 Processing helix chain 'k' and resid 5 through 16 removed outlier: 3.872A pdb=" N LYS k 16 " --> pdb=" O GLN k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 35 through 39 removed outlier: 3.783A pdb=" N LYS k 38 " --> pdb=" O PRO k 35 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE k 39 " --> pdb=" O ALA k 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 35 through 39' Processing helix chain 'k' and resid 42 through 50 removed outlier: 3.788A pdb=" N ASN k 50 " --> pdb=" O MET k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 106 through 109 removed outlier: 3.561A pdb=" N GLU k 109 " --> pdb=" O PRO k 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 106 through 109' Processing helix chain 'k' and resid 110 through 119 removed outlier: 3.588A pdb=" N PHE k 119 " --> pdb=" O VAL k 115 " (cutoff:3.500A) Processing helix chain 'k' and resid 154 through 159 Processing helix chain 'l' and resid 81 through 85 removed outlier: 3.706A pdb=" N ILE l 84 " --> pdb=" O LEU l 81 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS l 85 " --> pdb=" O LEU l 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 81 through 85' Processing helix chain 'l' and resid 90 through 105 removed outlier: 3.646A pdb=" N TYR l 96 " --> pdb=" O PRO l 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET l 98 " --> pdb=" O ALA l 94 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP l 101 " --> pdb=" O SER l 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU l 102 " --> pdb=" O MET l 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE l 104 " --> pdb=" O VAL l 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 109 through 137 removed outlier: 3.711A pdb=" N ARG l 124 " --> pdb=" O LEU l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 142 through 163 removed outlier: 3.547A pdb=" N ALA l 148 " --> pdb=" O ALA l 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG l 154 " --> pdb=" O ALA l 150 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE l 155 " --> pdb=" O TYR l 151 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN l 161 " --> pdb=" O ALA l 157 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU l 162 " --> pdb=" O LEU l 158 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 201 removed outlier: 3.957A pdb=" N GLN l 189 " --> pdb=" O LYS l 185 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG l 191 " --> pdb=" O LEU l 187 " (cutoff:3.500A) Processing helix chain 'l' and resid 204 through 209 Processing helix chain 'l' and resid 213 through 218 Processing helix chain 'l' and resid 247 through 252 Processing helix chain 'l' and resid 273 through 297 removed outlier: 4.588A pdb=" N ARG l 279 " --> pdb=" O ARG l 275 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP l 295 " --> pdb=" O GLU l 291 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET l 296 " --> pdb=" O GLN l 292 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY l 297 " --> pdb=" O LEU l 293 " (cutoff:3.500A) Processing helix chain 'l' and resid 307 through 311 removed outlier: 3.754A pdb=" N LEU l 310 " --> pdb=" O ASP l 307 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS l 311 " --> pdb=" O PRO l 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 307 through 311' Processing helix chain 'l' and resid 371 through 374 Processing helix chain 'l' and resid 375 through 382 Processing helix chain 'l' and resid 385 through 389 removed outlier: 3.673A pdb=" N ILE l 389 " --> pdb=" O PRO l 386 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 33 removed outlier: 4.816A pdb=" N ILE m 21 " --> pdb=" O PHE m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 52 removed outlier: 4.133A pdb=" N ILE m 46 " --> pdb=" O TYR m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 61 through 80 removed outlier: 3.845A pdb=" N ASP m 65 " --> pdb=" O GLY m 61 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE m 66 " --> pdb=" O LEU m 62 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE m 68 " --> pdb=" O TYR m 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU m 79 " --> pdb=" O THR m 75 " (cutoff:3.500A) Processing helix chain 'm' and resid 95 through 105 removed outlier: 3.927A pdb=" N GLU m 104 " --> pdb=" O THR m 100 " (cutoff:3.500A) Processing helix chain 'm' and resid 105 through 113 removed outlier: 4.259A pdb=" N MET m 111 " --> pdb=" O MET m 107 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA m 113 " --> pdb=" O GLY m 109 " (cutoff:3.500A) Processing helix chain 'm' and resid 119 through 136 removed outlier: 3.852A pdb=" N LEU m 131 " --> pdb=" O GLN m 127 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR m 132 " --> pdb=" O ARG m 128 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU m 133 " --> pdb=" O ALA m 129 " (cutoff:3.500A) Processing helix chain 'm' and resid 136 through 152 removed outlier: 3.908A pdb=" N LEU m 142 " --> pdb=" O VAL m 138 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR m 150 " --> pdb=" O ALA m 146 " (cutoff:3.500A) Processing helix chain 'm' and resid 156 through 166 removed outlier: 4.427A pdb=" N ALA m 162 " --> pdb=" O GLU m 158 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET m 166 " --> pdb=" O ALA m 162 " (cutoff:3.500A) Processing helix chain 'm' and resid 172 through 191 removed outlier: 3.552A pdb=" N LEU m 176 " --> pdb=" O HIS m 172 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA m 178 " --> pdb=" O PRO m 174 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA m 181 " --> pdb=" O LEU m 177 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN m 187 " --> pdb=" O ASP m 183 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA m 188 " --> pdb=" O ILE m 184 " (cutoff:3.500A) Processing helix chain 'm' and resid 192 through 196 removed outlier: 3.557A pdb=" N ASP m 196 " --> pdb=" O GLU m 193 " (cutoff:3.500A) Processing helix chain 'm' and resid 206 through 210 removed outlier: 3.739A pdb=" N MET m 209 " --> pdb=" O LEU m 206 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL m 210 " --> pdb=" O GLY m 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 206 through 210' Processing helix chain 'm' and resid 213 through 240 removed outlier: 3.511A pdb=" N ILE m 238 " --> pdb=" O PHE m 234 " (cutoff:3.500A) Processing helix chain 'm' and resid 252 through 277 removed outlier: 3.974A pdb=" N ALA m 257 " --> pdb=" O LEU m 253 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL m 269 " --> pdb=" O LYS m 265 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE m 275 " --> pdb=" O LEU m 271 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL m 276 " --> pdb=" O ILE m 272 " (cutoff:3.500A) Processing helix chain 'm' and resid 284 through 307 removed outlier: 3.692A pdb=" N TYR m 292 " --> pdb=" O ALA m 288 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP m 293 " --> pdb=" O ALA m 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS m 294 " --> pdb=" O LYS m 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP m 295 " --> pdb=" O PHE m 291 " (cutoff:3.500A) Proline residue: m 296 - end of helix Processing helix chain 'n' and resid 21 through 31 removed outlier: 4.070A pdb=" N LYS n 28 " --> pdb=" O PHE n 25 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR n 29 " --> pdb=" O GLY n 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU n 30 " --> pdb=" O LEU n 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE n 31 " --> pdb=" O LYS n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 70 removed outlier: 3.639A pdb=" N GLN n 69 " --> pdb=" O MET n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 132 removed outlier: 3.979A pdb=" N LEU n 129 " --> pdb=" O GLU n 126 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU n 130 " --> pdb=" O GLU n 127 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR n 131 " --> pdb=" O LEU n 128 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP n 132 " --> pdb=" O LEU n 129 " (cutoff:3.500A) Processing helix chain 'n' and resid 137 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 104 Processing sheet with id=AA2, first strand: chain 'H' and resid 59 through 62 removed outlier: 3.626A pdb=" N ILE H 59 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 54 through 56 removed outlier: 4.697A pdb=" N ILE X 54 " --> pdb=" O LEU X 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 21 through 22 removed outlier: 3.606A pdb=" N VAL J 22 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU J 61 " --> pdb=" O VAL J 22 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE J 60 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL J 87 " --> pdb=" O ASP J 117 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR J 119 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA J 89 " --> pdb=" O TYR J 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 22 through 25 removed outlier: 3.905A pdb=" N ARG K 25 " --> pdb=" O ARG K 29 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG K 29 " --> pdb=" O ARG K 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 54 through 60 removed outlier: 4.718A pdb=" N HIS K 73 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE K 57 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL K 71 " --> pdb=" O ILE K 57 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA K 59 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU K 69 " --> pdb=" O ALA K 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 54 through 60 removed outlier: 4.718A pdb=" N HIS K 73 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE K 57 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL K 71 " --> pdb=" O ILE K 57 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA K 59 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU K 69 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE K 89 " --> pdb=" O ILE K 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'L' and resid 29 through 30 removed outlier: 3.553A pdb=" N PHE L 30 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS L 53 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP L 47 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL L 51 " --> pdb=" O ASP L 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 321 through 327 removed outlier: 3.624A pdb=" N GLY L 321 " --> pdb=" O SER L 340 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA L 325 " --> pdb=" O ALA L 336 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL L 327 " --> pdb=" O PHE L 334 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG L 348 " --> pdb=" O VAL L 339 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 53 through 56 removed outlier: 3.918A pdb=" N GLY N 112 " --> pdb=" O THR N 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 166 through 168 removed outlier: 3.672A pdb=" N PHE N 179 " --> pdb=" O VAL N 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 102 through 104 Processing sheet with id=AB5, first strand: chain 'h' and resid 59 through 62 removed outlier: 3.627A pdb=" N ILE h 59 " --> pdb=" O ILE h 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'x' and resid 54 through 56 removed outlier: 4.697A pdb=" N ILE x 54 " --> pdb=" O LEU x 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 21 through 22 removed outlier: 3.606A pdb=" N VAL j 22 " --> pdb=" O LEU j 59 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU j 61 " --> pdb=" O VAL j 22 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE j 60 " --> pdb=" O LEU j 88 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL j 87 " --> pdb=" O ASP j 117 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR j 119 " --> pdb=" O VAL j 87 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA j 89 " --> pdb=" O TYR j 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'k' and resid 22 through 25 removed outlier: 3.906A pdb=" N ARG k 25 " --> pdb=" O ARG k 29 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG k 29 " --> pdb=" O ARG k 25 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'k' and resid 54 through 60 removed outlier: 4.718A pdb=" N HIS k 73 " --> pdb=" O LEU k 55 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE k 57 " --> pdb=" O VAL k 71 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL k 71 " --> pdb=" O ILE k 57 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA k 59 " --> pdb=" O GLU k 69 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU k 69 " --> pdb=" O ALA k 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'k' and resid 54 through 60 removed outlier: 4.718A pdb=" N HIS k 73 " --> pdb=" O LEU k 55 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE k 57 " --> pdb=" O VAL k 71 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL k 71 " --> pdb=" O ILE k 57 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA k 59 " --> pdb=" O GLU k 69 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU k 69 " --> pdb=" O ALA k 59 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE k 89 " --> pdb=" O ILE k 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'k' and resid 97 through 98 Processing sheet with id=AC3, first strand: chain 'l' and resid 29 through 30 removed outlier: 3.554A pdb=" N PHE l 30 " --> pdb=" O ILE l 42 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS l 53 " --> pdb=" O LYS l 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP l 47 " --> pdb=" O VAL l 51 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL l 51 " --> pdb=" O ASP l 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'l' and resid 321 through 327 removed outlier: 3.624A pdb=" N GLY l 321 " --> pdb=" O SER l 340 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA l 325 " --> pdb=" O ALA l 336 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL l 327 " --> pdb=" O PHE l 334 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG l 348 " --> pdb=" O VAL l 339 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'n' and resid 53 through 56 removed outlier: 3.919A pdb=" N GLY n 112 " --> pdb=" O THR n 55 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'n' and resid 166 through 168 removed outlier: 3.672A pdb=" N PHE n 179 " --> pdb=" O VAL n 167 " (cutoff:3.500A) 2247 hydrogen bonds defined for protein. 6561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.06 Time building geometry restraints manager: 10.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 20555 1.43 - 1.64: 28563 1.64 - 1.85: 434 1.85 - 2.06: 0 2.06 - 2.27: 72 Bond restraints: 49624 Sorted by residual: bond pdb=" C PRO j 34 " pdb=" N PRO j 35 " ideal model delta sigma weight residual 1.337 1.395 -0.058 1.11e-02 8.12e+03 2.76e+01 bond pdb=" C PRO J 34 " pdb=" N PRO J 35 " ideal model delta sigma weight residual 1.337 1.394 -0.058 1.11e-02 8.12e+03 2.69e+01 bond pdb=" CA CYS N 102 " pdb=" C CYS N 102 " ideal model delta sigma weight residual 1.522 1.459 0.063 1.37e-02 5.33e+03 2.14e+01 bond pdb=" C ILE e 209 " pdb=" N PRO e 210 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.04e+01 bond pdb=" C ILE E 209 " pdb=" N PRO E 210 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.00e+01 ... (remaining 49619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 66100 3.57 - 7.15: 1159 7.15 - 10.72: 181 10.72 - 14.30: 17 14.30 - 17.87: 1 Bond angle restraints: 67458 Sorted by residual: angle pdb=" C LEU e 203 " pdb=" CA LEU e 203 " pdb=" CB LEU e 203 " ideal model delta sigma weight residual 109.37 91.50 17.87 1.83e+00 2.99e-01 9.54e+01 angle pdb=" N GLY E 201 " pdb=" CA GLY E 201 " pdb=" C GLY E 201 " ideal model delta sigma weight residual 112.55 99.48 13.07 1.44e+00 4.82e-01 8.23e+01 angle pdb=" N VAL h 104 " pdb=" CA VAL h 104 " pdb=" C VAL h 104 " ideal model delta sigma weight residual 113.71 105.91 7.80 9.50e-01 1.11e+00 6.74e+01 angle pdb=" N VAL H 104 " pdb=" CA VAL H 104 " pdb=" C VAL H 104 " ideal model delta sigma weight residual 113.71 105.94 7.77 9.50e-01 1.11e+00 6.69e+01 angle pdb=" C LYS M 192 " pdb=" N GLU M 193 " pdb=" CA GLU M 193 " ideal model delta sigma weight residual 120.09 128.89 -8.80 1.25e+00 6.40e-01 4.96e+01 ... (remaining 67453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 25323 17.83 - 35.67: 2907 35.67 - 53.50: 594 53.50 - 71.34: 84 71.34 - 89.17: 40 Dihedral angle restraints: 28948 sinusoidal: 11268 harmonic: 17680 Sorted by residual: dihedral pdb=" CA ASN X 486 " pdb=" C ASN X 486 " pdb=" N PRO X 487 " pdb=" CA PRO X 487 " ideal model delta harmonic sigma weight residual -180.00 -132.58 -47.42 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA ASN x 486 " pdb=" C ASN x 486 " pdb=" N PRO x 487 " pdb=" CA PRO x 487 " ideal model delta harmonic sigma weight residual 180.00 -132.59 -47.41 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA THR A 123 " pdb=" C THR A 123 " pdb=" N PRO A 124 " pdb=" CA PRO A 124 " ideal model delta harmonic sigma weight residual -180.00 -133.25 -46.75 0 5.00e+00 4.00e-02 8.74e+01 ... (remaining 28945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 7047 0.106 - 0.212: 664 0.212 - 0.319: 42 0.319 - 0.425: 11 0.425 - 0.531: 4 Chirality restraints: 7768 Sorted by residual: chirality pdb=" CB ILE n 76 " pdb=" CA ILE n 76 " pdb=" CG1 ILE n 76 " pdb=" CG2 ILE n 76 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" CB ILE N 76 " pdb=" CA ILE N 76 " pdb=" CG1 ILE N 76 " pdb=" CG2 ILE N 76 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CB ILE A 42 " pdb=" CA ILE A 42 " pdb=" CG1 ILE A 42 " pdb=" CG2 ILE A 42 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 7765 not shown) Planarity restraints: 8248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY j 144 " -0.032 2.00e-02 2.50e+03 6.19e-02 3.83e+01 pdb=" C GLY j 144 " 0.107 2.00e-02 2.50e+03 pdb=" O GLY j 144 " -0.040 2.00e-02 2.50e+03 pdb=" N GLU j 145 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 144 " 0.032 2.00e-02 2.50e+03 6.18e-02 3.82e+01 pdb=" C GLY J 144 " -0.107 2.00e-02 2.50e+03 pdb=" O GLY J 144 " 0.040 2.00e-02 2.50e+03 pdb=" N GLU J 145 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR d 80 " -0.031 2.00e-02 2.50e+03 6.07e-02 3.69e+01 pdb=" C TYR d 80 " 0.105 2.00e-02 2.50e+03 pdb=" O TYR d 80 " -0.040 2.00e-02 2.50e+03 pdb=" N GLU d 81 " -0.034 2.00e-02 2.50e+03 ... (remaining 8245 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 6811 2.75 - 3.29: 47353 3.29 - 3.82: 83463 3.82 - 4.36: 97100 4.36 - 4.90: 163953 Nonbonded interactions: 398680 Sorted by model distance: nonbonded pdb=" OG1 THR X 537 " pdb=" OE2 GLU M 211 " model vdw 2.209 3.040 nonbonded pdb=" O TYR e 170 " pdb=" OG1 THR e 173 " model vdw 2.248 3.040 nonbonded pdb=" O TYR E 170 " pdb=" OG1 THR E 173 " model vdw 2.248 3.040 nonbonded pdb=" O ILE a 120 " pdb=" OG1 THR a 126 " model vdw 2.259 3.040 nonbonded pdb=" O ILE A 120 " pdb=" OG1 THR A 126 " model vdw 2.259 3.040 ... (remaining 398675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'X' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.360 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 87.740 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 49624 Z= 0.504 Angle : 1.209 17.871 67458 Z= 0.665 Chirality : 0.065 0.531 7768 Planarity : 0.009 0.090 8248 Dihedral : 15.795 89.169 17668 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.14 % Favored : 87.53 % Rotamer: Outliers : 2.01 % Allowed : 12.55 % Favored : 85.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 2.14 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.88 (0.07), residues: 6072 helix: -3.56 (0.05), residues: 3432 sheet: -3.48 (0.28), residues: 186 loop : -4.34 (0.10), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 149 HIS 0.008 0.002 HIS h 330 PHE 0.046 0.003 PHE H 247 TYR 0.023 0.003 TYR J 113 ARG 0.012 0.001 ARG K 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1483 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1382 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.7715 (t0) cc_final: 0.7124 (t0) REVERT: A 131 VAL cc_start: 0.8176 (t) cc_final: 0.7972 (t) REVERT: C 10 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7516 (mp) REVERT: C 18 PHE cc_start: 0.7411 (t80) cc_final: 0.6885 (t80) REVERT: C 89 LEU cc_start: 0.8148 (tp) cc_final: 0.7930 (tp) REVERT: D 21 LEU cc_start: 0.8956 (mm) cc_final: 0.8226 (mm) REVERT: D 46 PHE cc_start: 0.8681 (m-10) cc_final: 0.8366 (m-80) REVERT: E 147 LEU cc_start: 0.9099 (tp) cc_final: 0.8727 (tp) REVERT: E 219 LYS cc_start: 0.9035 (tttp) cc_final: 0.8618 (tmmt) REVERT: E 225 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8246 (p) REVERT: G 100 LYS cc_start: 0.8990 (mmtm) cc_final: 0.8714 (mmtt) REVERT: H 112 MET cc_start: 0.7202 (ptp) cc_final: 0.6570 (ptp) REVERT: H 254 TYR cc_start: 0.7901 (t80) cc_final: 0.7417 (t80) REVERT: H 300 MET cc_start: 0.7709 (ttt) cc_final: 0.7289 (ttt) REVERT: H 422 TYR cc_start: 0.8443 (p90) cc_final: 0.7555 (p90) REVERT: H 450 LEU cc_start: 0.8221 (mm) cc_final: 0.7991 (mm) REVERT: H 454 MET cc_start: 0.7198 (mmp) cc_final: 0.6697 (ttp) REVERT: X 216 VAL cc_start: 0.8798 (m) cc_final: 0.8160 (t) REVERT: X 318 ILE cc_start: 0.8982 (mt) cc_final: 0.8714 (mt) REVERT: X 379 MET cc_start: 0.7319 (mmt) cc_final: 0.6857 (mmt) REVERT: X 434 TYR cc_start: 0.7745 (t80) cc_final: 0.7309 (t80) REVERT: X 507 LEU cc_start: 0.7166 (tp) cc_final: 0.6593 (tp) REVERT: X 552 ILE cc_start: 0.9271 (pt) cc_final: 0.8996 (pt) REVERT: J 57 TYR cc_start: 0.8847 (p90) cc_final: 0.8618 (p90) REVERT: J 93 CYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7241 (m) REVERT: J 102 ASP cc_start: 0.7361 (t0) cc_final: 0.7128 (t0) REVERT: K 110 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9038 (t) REVERT: K 145 HIS cc_start: 0.7947 (m-70) cc_final: 0.7516 (m170) REVERT: L 33 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8792 (tm-30) REVERT: L 82 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9139 (mm) REVERT: L 96 TYR cc_start: 0.8959 (t80) cc_final: 0.8707 (t80) REVERT: L 133 MET cc_start: 0.8110 (tmm) cc_final: 0.7900 (tmm) REVERT: L 189 GLN cc_start: 0.7960 (tp40) cc_final: 0.7739 (tp40) REVERT: L 280 ARG cc_start: 0.8026 (ttt-90) cc_final: 0.7751 (ttt90) REVERT: L 333 ASP cc_start: 0.7838 (t0) cc_final: 0.7005 (p0) REVERT: M 35 ARG cc_start: 0.8584 (mtt-85) cc_final: 0.8257 (mtp85) REVERT: M 104 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7180 (mt-10) REVERT: M 169 SER cc_start: 0.7872 (t) cc_final: 0.7609 (t) REVERT: M 198 MET cc_start: 0.6927 (pmm) cc_final: 0.6663 (pmm) REVERT: M 290 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8140 (tptt) REVERT: N 30 LEU cc_start: 0.9023 (mt) cc_final: 0.8763 (mt) REVERT: N 92 ASP cc_start: 0.8545 (p0) cc_final: 0.8269 (p0) REVERT: a 126 THR cc_start: 0.6852 (p) cc_final: 0.5763 (p) REVERT: a 130 ASP cc_start: 0.7817 (t0) cc_final: 0.7496 (t0) REVERT: d 14 LEU cc_start: 0.8957 (tp) cc_final: 0.8724 (tp) REVERT: d 21 LEU cc_start: 0.9052 (mm) cc_final: 0.8817 (mm) REVERT: d 70 PHE cc_start: 0.8011 (t80) cc_final: 0.7485 (t80) REVERT: e 147 LEU cc_start: 0.9282 (tp) cc_final: 0.9059 (tp) REVERT: e 219 LYS cc_start: 0.9223 (tttp) cc_final: 0.8680 (tmmt) REVERT: g 24 LYS cc_start: 0.8086 (mttt) cc_final: 0.7853 (mttp) REVERT: g 36 MET cc_start: 0.7773 (ttt) cc_final: 0.7537 (ttt) REVERT: g 37 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7499 (mm-30) REVERT: g 69 ASP cc_start: 0.6505 (p0) cc_final: 0.6238 (p0) REVERT: g 77 LEU cc_start: 0.8615 (tp) cc_final: 0.8355 (tp) REVERT: g 100 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8620 (mmtt) REVERT: h 104 VAL cc_start: 0.6776 (OUTLIER) cc_final: 0.6520 (p) REVERT: h 112 MET cc_start: 0.7105 (ptp) cc_final: 0.6537 (ptp) REVERT: h 119 LEU cc_start: 0.8245 (tt) cc_final: 0.8045 (tp) REVERT: h 158 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8263 (tm-30) REVERT: h 254 TYR cc_start: 0.7994 (t80) cc_final: 0.7472 (t80) REVERT: h 422 TYR cc_start: 0.8488 (p90) cc_final: 0.7698 (p90) REVERT: h 454 MET cc_start: 0.7038 (mmp) cc_final: 0.6607 (ttp) REVERT: x 216 VAL cc_start: 0.8774 (m) cc_final: 0.8181 (t) REVERT: x 300 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8141 (tp-100) REVERT: x 318 ILE cc_start: 0.8953 (mt) cc_final: 0.8739 (mt) REVERT: x 369 LEU cc_start: 0.8711 (tp) cc_final: 0.8475 (tt) REVERT: x 373 MET cc_start: 0.7783 (ptp) cc_final: 0.7533 (ptp) REVERT: x 379 MET cc_start: 0.7318 (mmt) cc_final: 0.6862 (mmt) REVERT: x 434 TYR cc_start: 0.7722 (t80) cc_final: 0.7210 (t80) REVERT: x 507 LEU cc_start: 0.7275 (tp) cc_final: 0.6703 (tp) REVERT: j 93 CYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7652 (m) REVERT: k 145 HIS cc_start: 0.7894 (m-70) cc_final: 0.7409 (m-70) REVERT: l 33 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8749 (tm-30) REVERT: l 82 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8960 (mm) REVERT: l 93 GLU cc_start: 0.8003 (pt0) cc_final: 0.7715 (pt0) REVERT: l 96 TYR cc_start: 0.8855 (t80) cc_final: 0.8602 (t80) REVERT: l 133 MET cc_start: 0.8248 (tmm) cc_final: 0.8021 (tmm) REVERT: l 215 TYR cc_start: 0.7532 (t80) cc_final: 0.7293 (t80) REVERT: l 280 ARG cc_start: 0.7935 (ttt-90) cc_final: 0.7533 (ttt90) REVERT: l 333 ASP cc_start: 0.7913 (t0) cc_final: 0.6547 (p0) REVERT: m 35 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8318 (mtp85) REVERT: m 49 LEU cc_start: 0.9139 (tp) cc_final: 0.8883 (tp) REVERT: m 169 SER cc_start: 0.7820 (t) cc_final: 0.7571 (t) REVERT: m 193 GLU cc_start: 0.8370 (tp30) cc_final: 0.8150 (tp30) REVERT: m 290 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8173 (tptt) REVERT: n 66 MET cc_start: 0.8356 (tpt) cc_final: 0.8129 (tpt) REVERT: n 92 ASP cc_start: 0.8555 (p0) cc_final: 0.8280 (p0) outliers start: 101 outliers final: 35 residues processed: 1455 average time/residue: 0.5128 time to fit residues: 1227.7868 Evaluate side-chains 1052 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1009 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain J residue 25 CYS Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain c residue 34 ASN Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain e residue 200 ILE Chi-restraints excluded: chain h residue 61 ILE Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain j residue 93 CYS Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 510 optimal weight: 3.9990 chunk 457 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 473 optimal weight: 0.0670 chunk 183 optimal weight: 0.8980 chunk 287 optimal weight: 0.0370 chunk 352 optimal weight: 10.0000 chunk 548 optimal weight: 20.0000 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 91 HIS ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 GLN ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 466 ASN J 109 GLN K 73 HIS L 39 ASN L 292 GLN L 326 HIS ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN M 57 ASN ** M 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 HIS N 145 GLN a 58 ASN ** g 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 308 GLN x 340 HIS x 466 ASN ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 73 HIS l 39 ASN l 292 GLN l 326 HIS ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 43 GLN m 57 ASN ** m 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 187 GLN n 54 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 49624 Z= 0.225 Angle : 0.794 13.618 67458 Z= 0.402 Chirality : 0.045 0.276 7768 Planarity : 0.006 0.074 8248 Dihedral : 6.889 59.961 6699 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.64 % Favored : 89.23 % Rotamer: Outliers : 4.03 % Allowed : 19.84 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.09), residues: 6072 helix: -1.88 (0.08), residues: 3494 sheet: -3.46 (0.29), residues: 200 loop : -4.01 (0.11), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 149 HIS 0.008 0.001 HIS c 87 PHE 0.027 0.002 PHE x 343 TYR 0.028 0.002 TYR k 154 ARG 0.009 0.001 ARG x 502 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1317 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1114 time to evaluate : 4.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7616 (t-100) cc_final: 0.7392 (t60) REVERT: A 130 ASP cc_start: 0.7562 (t0) cc_final: 0.7193 (t0) REVERT: B 76 PHE cc_start: 0.7158 (m-80) cc_final: 0.6840 (m-80) REVERT: C 10 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7510 (mp) REVERT: D 46 PHE cc_start: 0.8508 (m-10) cc_final: 0.8305 (m-80) REVERT: D 47 PHE cc_start: 0.8849 (t80) cc_final: 0.8629 (t80) REVERT: E 120 ILE cc_start: 0.8315 (mm) cc_final: 0.7981 (mt) REVERT: E 145 MET cc_start: 0.7974 (tpt) cc_final: 0.7418 (tpp) REVERT: E 147 LEU cc_start: 0.9164 (tp) cc_final: 0.8888 (tp) REVERT: E 193 TRP cc_start: 0.4295 (p-90) cc_final: 0.3619 (m-10) REVERT: E 225 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8160 (p) REVERT: H 37 ILE cc_start: 0.8805 (mm) cc_final: 0.8543 (tp) REVERT: H 79 PHE cc_start: 0.8344 (t80) cc_final: 0.7823 (t80) REVERT: H 112 MET cc_start: 0.7290 (ptp) cc_final: 0.6346 (ptp) REVERT: H 254 TYR cc_start: 0.8315 (t80) cc_final: 0.7769 (t80) REVERT: H 300 MET cc_start: 0.7604 (ttt) cc_final: 0.7301 (ttt) REVERT: H 358 GLU cc_start: 0.6793 (mp0) cc_final: 0.6248 (mp0) REVERT: H 422 TYR cc_start: 0.8508 (p90) cc_final: 0.7743 (p90) REVERT: H 454 MET cc_start: 0.6972 (mmp) cc_final: 0.6395 (tmm) REVERT: X 130 MET cc_start: 0.8040 (tmm) cc_final: 0.7831 (ppp) REVERT: X 216 VAL cc_start: 0.8651 (m) cc_final: 0.8084 (t) REVERT: X 379 MET cc_start: 0.7328 (mmt) cc_final: 0.7112 (mmt) REVERT: X 524 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: X 552 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8664 (pt) REVERT: K 69 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7923 (mt-10) REVERT: K 98 MET cc_start: 0.8326 (tpp) cc_final: 0.8097 (tpp) REVERT: K 110 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8682 (t) REVERT: K 145 HIS cc_start: 0.7840 (m-70) cc_final: 0.7325 (m-70) REVERT: L 26 TYR cc_start: 0.8760 (p90) cc_final: 0.8407 (p90) REVERT: L 33 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8783 (tm-30) REVERT: L 66 GLU cc_start: 0.7200 (tt0) cc_final: 0.5672 (tt0) REVERT: L 82 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9074 (mm) REVERT: L 83 ARG cc_start: 0.8514 (mpt90) cc_final: 0.8260 (mpt180) REVERT: L 96 TYR cc_start: 0.8814 (t80) cc_final: 0.8581 (t80) REVERT: L 133 MET cc_start: 0.8186 (tmm) cc_final: 0.7810 (tmm) REVERT: L 160 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7348 (tm-30) REVERT: L 168 TYR cc_start: 0.7940 (m-10) cc_final: 0.7665 (m-80) REVERT: L 384 ASN cc_start: 0.7801 (m-40) cc_final: 0.7445 (t0) REVERT: M 35 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.8244 (mtp85) REVERT: M 104 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7058 (mt-10) REVERT: M 137 GLN cc_start: 0.7998 (mm110) cc_final: 0.7341 (mm-40) REVERT: M 157 TYR cc_start: 0.6681 (t80) cc_final: 0.6462 (t80) REVERT: M 158 GLU cc_start: 0.8070 (mp0) cc_final: 0.7741 (mm-30) REVERT: M 209 MET cc_start: 0.8193 (pmm) cc_final: 0.7665 (pmm) REVERT: M 290 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8028 (tptt) REVERT: M 295 TRP cc_start: 0.8287 (m100) cc_final: 0.7928 (m100) REVERT: N 81 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7716 (mm) REVERT: a 91 HIS cc_start: 0.4314 (OUTLIER) cc_final: 0.4012 (t-170) REVERT: a 118 ASN cc_start: 0.7939 (m-40) cc_final: 0.7697 (m110) REVERT: b 67 ILE cc_start: 0.7920 (mp) cc_final: 0.7629 (tp) REVERT: c 35 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7803 (ttm110) REVERT: e 145 MET cc_start: 0.7943 (tpt) cc_final: 0.7379 (tpp) REVERT: e 147 LEU cc_start: 0.9279 (tp) cc_final: 0.9072 (tp) REVERT: e 219 LYS cc_start: 0.9104 (tttp) cc_final: 0.8393 (tmmt) REVERT: e 233 LYS cc_start: 0.8808 (mmtp) cc_final: 0.8300 (mmmm) REVERT: g 24 LYS cc_start: 0.8019 (mttt) cc_final: 0.7551 (tttp) REVERT: g 41 ASN cc_start: 0.9055 (p0) cc_final: 0.8796 (p0) REVERT: g 100 LYS cc_start: 0.8897 (mmtm) cc_final: 0.8637 (mmtt) REVERT: h 79 PHE cc_start: 0.8285 (t80) cc_final: 0.7739 (t80) REVERT: h 104 VAL cc_start: 0.6347 (OUTLIER) cc_final: 0.6131 (p) REVERT: h 112 MET cc_start: 0.7045 (ptp) cc_final: 0.6198 (ptp) REVERT: h 145 TYR cc_start: 0.7722 (m-10) cc_final: 0.7493 (m-10) REVERT: h 158 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8286 (tm-30) REVERT: h 254 TYR cc_start: 0.8356 (t80) cc_final: 0.7857 (t80) REVERT: h 422 TYR cc_start: 0.8553 (p90) cc_final: 0.7683 (p90) REVERT: x 130 MET cc_start: 0.8145 (tmm) cc_final: 0.7908 (ppp) REVERT: x 216 VAL cc_start: 0.8661 (m) cc_final: 0.8122 (t) REVERT: x 305 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8426 (ttpp) REVERT: x 379 MET cc_start: 0.7383 (mmt) cc_final: 0.6621 (mmt) REVERT: x 404 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7862 (mm-30) REVERT: x 524 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: k 145 HIS cc_start: 0.7769 (m-70) cc_final: 0.7398 (m170) REVERT: l 26 TYR cc_start: 0.8843 (p90) cc_final: 0.8469 (p90) REVERT: l 33 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8749 (tm-30) REVERT: l 82 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8923 (mm) REVERT: l 113 GLN cc_start: 0.8614 (mm110) cc_final: 0.8410 (mm110) REVERT: l 133 MET cc_start: 0.8275 (tmm) cc_final: 0.7959 (tmm) REVERT: l 197 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8981 (tt) REVERT: m 69 ILE cc_start: 0.8633 (mm) cc_final: 0.8339 (tp) REVERT: m 157 TYR cc_start: 0.6836 (t80) cc_final: 0.6472 (t80) REVERT: m 158 GLU cc_start: 0.8001 (mp0) cc_final: 0.7663 (mm-30) REVERT: m 186 LEU cc_start: 0.9050 (mt) cc_final: 0.8778 (tt) REVERT: m 209 MET cc_start: 0.8282 (pmm) cc_final: 0.7880 (pmm) REVERT: m 290 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8090 (tptt) REVERT: n 81 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7137 (tp) REVERT: n 141 PHE cc_start: 0.8221 (t80) cc_final: 0.8013 (t80) outliers start: 203 outliers final: 97 residues processed: 1234 average time/residue: 0.4848 time to fit residues: 1027.7912 Evaluate side-chains 1085 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 974 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 70 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 419 PHE Chi-restraints excluded: chain X residue 506 LEU Chi-restraints excluded: chain X residue 524 PHE Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 552 ILE Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 297 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 73 TYR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain b residue 70 PHE Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 90 ILE Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 193 TRP Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 412 VAL Chi-restraints excluded: chain h residue 417 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 419 PHE Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 506 LEU Chi-restraints excluded: chain x residue 524 PHE Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 154 GLU Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 136 SER Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 349 VAL Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 297 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 456 optimal weight: 4.9990 chunk 373 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 549 optimal weight: 0.9990 chunk 593 optimal weight: 1.9990 chunk 489 optimal weight: 3.9990 chunk 544 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 440 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 ASN ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 314 GLN X 340 HIS ** J 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 HIS ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 62 HIS ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 GLN ** M 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 224 HIS N 100 GLN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 189 ASN x 340 HIS ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN l 62 HIS ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 163 GLN m 172 HIS m 224 HIS m 237 ASN ** m 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 49624 Z= 0.279 Angle : 0.770 11.728 67458 Z= 0.388 Chirality : 0.045 0.216 7768 Planarity : 0.006 0.061 8248 Dihedral : 6.464 58.817 6678 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.23 % Favored : 88.69 % Rotamer: Outliers : 5.10 % Allowed : 21.84 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.10), residues: 6072 helix: -1.16 (0.08), residues: 3496 sheet: -3.39 (0.32), residues: 192 loop : -3.83 (0.11), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 21 HIS 0.007 0.001 HIS c 87 PHE 0.035 0.002 PHE h 247 TYR 0.033 0.002 TYR E 152 ARG 0.011 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1045 time to evaluate : 4.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7602 (t-100) cc_final: 0.7379 (t60) REVERT: A 114 MET cc_start: 0.7519 (mtt) cc_final: 0.7152 (ttm) REVERT: C 10 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7747 (mp) REVERT: E 108 LEU cc_start: 0.8403 (tt) cc_final: 0.8078 (tp) REVERT: E 120 ILE cc_start: 0.8478 (mm) cc_final: 0.8103 (mt) REVERT: E 145 MET cc_start: 0.7851 (tpt) cc_final: 0.7596 (tpp) REVERT: E 193 TRP cc_start: 0.4144 (p-90) cc_final: 0.3683 (m-10) REVERT: E 199 ASN cc_start: 0.7315 (p0) cc_final: 0.7066 (p0) REVERT: G 99 GLU cc_start: 0.7548 (tp30) cc_final: 0.7306 (tp30) REVERT: H 37 ILE cc_start: 0.8748 (mm) cc_final: 0.8495 (tp) REVERT: H 79 PHE cc_start: 0.8398 (t80) cc_final: 0.7966 (t80) REVERT: H 94 MET cc_start: 0.6866 (mmp) cc_final: 0.6577 (mmp) REVERT: H 96 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7666 (tp) REVERT: H 112 MET cc_start: 0.7274 (ptp) cc_final: 0.6351 (ptp) REVERT: H 190 MET cc_start: 0.8881 (mtt) cc_final: 0.8602 (mtm) REVERT: H 254 TYR cc_start: 0.8240 (t80) cc_final: 0.7770 (t80) REVERT: H 300 MET cc_start: 0.7579 (ttt) cc_final: 0.7202 (ttt) REVERT: H 331 MET cc_start: 0.8623 (tpp) cc_final: 0.8375 (tpp) REVERT: H 422 TYR cc_start: 0.8617 (p90) cc_final: 0.7799 (p90) REVERT: H 454 MET cc_start: 0.6991 (mmp) cc_final: 0.6434 (tmm) REVERT: X 130 MET cc_start: 0.8272 (tmm) cc_final: 0.7908 (ppp) REVERT: X 216 VAL cc_start: 0.8672 (m) cc_final: 0.8088 (t) REVERT: X 373 MET cc_start: 0.7445 (ptp) cc_final: 0.7181 (ptp) REVERT: X 379 MET cc_start: 0.7378 (mmt) cc_final: 0.7131 (mmt) REVERT: X 552 ILE cc_start: 0.9227 (pt) cc_final: 0.8968 (pt) REVERT: X 591 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7618 (ttt90) REVERT: J 57 TYR cc_start: 0.8967 (p90) cc_final: 0.8676 (p90) REVERT: J 119 TYR cc_start: 0.8965 (m-80) cc_final: 0.8760 (m-80) REVERT: K 50 ASN cc_start: 0.7734 (p0) cc_final: 0.7405 (p0) REVERT: K 110 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8729 (t) REVERT: K 145 HIS cc_start: 0.7665 (m-70) cc_final: 0.7282 (m170) REVERT: L 33 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8844 (tm-30) REVERT: L 93 GLU cc_start: 0.8133 (pt0) cc_final: 0.7368 (pt0) REVERT: L 96 TYR cc_start: 0.8968 (t80) cc_final: 0.8705 (t80) REVERT: L 133 MET cc_start: 0.8230 (tmm) cc_final: 0.7785 (tmm) REVERT: L 160 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7445 (tm-30) REVERT: M 35 ARG cc_start: 0.8544 (mtt-85) cc_final: 0.8236 (mtp85) REVERT: M 103 LEU cc_start: 0.8754 (mm) cc_final: 0.8405 (mp) REVERT: M 104 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7126 (mt-10) REVERT: M 137 GLN cc_start: 0.8279 (mm110) cc_final: 0.7796 (mm110) REVERT: M 158 GLU cc_start: 0.7975 (mp0) cc_final: 0.7756 (mm-30) REVERT: M 209 MET cc_start: 0.8083 (pmm) cc_final: 0.7792 (pmm) REVERT: M 290 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8099 (tptt) REVERT: M 295 TRP cc_start: 0.8378 (m100) cc_final: 0.7985 (m100) REVERT: N 81 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7400 (tp) REVERT: N 136 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8495 (pt) REVERT: a 91 HIS cc_start: 0.4368 (OUTLIER) cc_final: 0.4040 (t-170) REVERT: b 67 ILE cc_start: 0.7914 (mt) cc_final: 0.7574 (tp) REVERT: c 19 TYR cc_start: 0.7012 (m-80) cc_final: 0.6640 (m-80) REVERT: c 36 MET cc_start: 0.8857 (ppp) cc_final: 0.8476 (ppp) REVERT: d 70 PHE cc_start: 0.7751 (t80) cc_final: 0.7267 (t80) REVERT: e 145 MET cc_start: 0.7552 (tpt) cc_final: 0.7231 (tpp) REVERT: e 146 TYR cc_start: 0.8004 (t80) cc_final: 0.7153 (t80) REVERT: e 168 MET cc_start: 0.5542 (mtt) cc_final: 0.4945 (mtp) REVERT: e 219 LYS cc_start: 0.9084 (tttp) cc_final: 0.8806 (ttpp) REVERT: e 223 GLU cc_start: 0.6947 (tp30) cc_final: 0.6585 (tp30) REVERT: g 41 ASN cc_start: 0.9109 (p0) cc_final: 0.8875 (p0) REVERT: g 100 LYS cc_start: 0.8960 (mmtm) cc_final: 0.8734 (mmtt) REVERT: h 18 PHE cc_start: 0.6849 (t80) cc_final: 0.6513 (t80) REVERT: h 37 ILE cc_start: 0.8817 (mm) cc_final: 0.8588 (tp) REVERT: h 79 PHE cc_start: 0.8350 (t80) cc_final: 0.7993 (t80) REVERT: h 94 MET cc_start: 0.6801 (mmp) cc_final: 0.6491 (mmp) REVERT: h 96 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7501 (tp) REVERT: h 112 MET cc_start: 0.7125 (ptp) cc_final: 0.6254 (ptp) REVERT: h 158 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8309 (tm-30) REVERT: h 190 MET cc_start: 0.8926 (mtt) cc_final: 0.8637 (mtm) REVERT: h 254 TYR cc_start: 0.8257 (t80) cc_final: 0.7813 (t80) REVERT: h 289 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8797 (tt) REVERT: h 422 TYR cc_start: 0.8660 (p90) cc_final: 0.7840 (p90) REVERT: h 467 TRP cc_start: 0.8608 (t-100) cc_final: 0.8264 (t-100) REVERT: x 130 MET cc_start: 0.8321 (tmm) cc_final: 0.7963 (ppp) REVERT: x 216 VAL cc_start: 0.8650 (m) cc_final: 0.8126 (t) REVERT: x 300 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8558 (tp-100) REVERT: x 305 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8227 (ttpp) REVERT: x 379 MET cc_start: 0.7616 (mmt) cc_final: 0.7399 (mmt) REVERT: x 404 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7923 (mm-30) REVERT: x 591 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7663 (ttt90) REVERT: k 131 MET cc_start: 0.7420 (ttm) cc_final: 0.7178 (ttm) REVERT: k 145 HIS cc_start: 0.7754 (m-70) cc_final: 0.7370 (m170) REVERT: l 33 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8804 (tm-30) REVERT: l 82 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.8982 (mm) REVERT: l 133 MET cc_start: 0.8339 (tmm) cc_final: 0.7974 (tmm) REVERT: l 333 ASP cc_start: 0.7569 (t0) cc_final: 0.7198 (p0) REVERT: m 69 ILE cc_start: 0.8636 (mm) cc_final: 0.8291 (tp) REVERT: m 133 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8568 (tp) REVERT: m 158 GLU cc_start: 0.8081 (mp0) cc_final: 0.7768 (mm-30) REVERT: m 186 LEU cc_start: 0.9042 (mt) cc_final: 0.8772 (tt) REVERT: m 209 MET cc_start: 0.8109 (pmm) cc_final: 0.7900 (pmm) REVERT: m 290 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8149 (tptt) REVERT: n 74 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8400 (tpt90) REVERT: n 132 ASP cc_start: 0.7568 (t0) cc_final: 0.6989 (t70) outliers start: 257 outliers final: 153 residues processed: 1210 average time/residue: 0.4640 time to fit residues: 958.9918 Evaluate side-chains 1129 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 962 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 66 TYR Chi-restraints excluded: chain A residue 73 TYR Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 312 ILE Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 419 PHE Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 591 ARG Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain M residue 297 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 136 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 96 LEU Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 312 ILE Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 417 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 340 HIS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 419 PHE Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 506 LEU Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 552 ILE Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 114 ILE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 154 GLU Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 136 SER Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 349 VAL Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 542 optimal weight: 8.9990 chunk 413 optimal weight: 10.0000 chunk 285 optimal weight: 0.0980 chunk 60 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 368 optimal weight: 5.9990 chunk 551 optimal weight: 2.9990 chunk 583 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 522 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 340 HIS J 163 GLN L 39 ASN L 384 ASN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 237 ASN ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 340 HIS ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 237 ASN ** m 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 49624 Z= 0.269 Angle : 0.748 12.046 67458 Z= 0.375 Chirality : 0.045 0.209 7768 Planarity : 0.005 0.064 8248 Dihedral : 6.250 59.577 6671 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.30 % Favored : 88.62 % Rotamer: Outliers : 5.66 % Allowed : 23.37 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.10), residues: 6072 helix: -0.78 (0.09), residues: 3480 sheet: -3.30 (0.30), residues: 246 loop : -3.77 (0.11), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 21 HIS 0.007 0.001 HIS x 336 PHE 0.031 0.002 PHE X 255 TYR 0.036 0.002 TYR G 5 ARG 0.010 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1016 time to evaluate : 4.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7614 (t-100) cc_final: 0.7340 (t60) REVERT: A 78 MET cc_start: 0.8171 (mpp) cc_final: 0.7923 (mtt) REVERT: B 49 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.7105 (m-10) REVERT: B 64 VAL cc_start: 0.8692 (t) cc_final: 0.8416 (t) REVERT: B 67 ILE cc_start: 0.7780 (mp) cc_final: 0.7401 (tp) REVERT: C 10 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7672 (mp) REVERT: C 18 PHE cc_start: 0.7258 (t80) cc_final: 0.6684 (t80) REVERT: C 77 PHE cc_start: 0.6948 (t80) cc_final: 0.6651 (t80) REVERT: D 70 PHE cc_start: 0.7767 (t80) cc_final: 0.7551 (t80) REVERT: E 120 ILE cc_start: 0.8465 (mm) cc_final: 0.8082 (mt) REVERT: E 145 MET cc_start: 0.7715 (tpt) cc_final: 0.7433 (tpp) REVERT: E 146 TYR cc_start: 0.7991 (t80) cc_final: 0.7204 (t80) REVERT: E 193 TRP cc_start: 0.4228 (p-90) cc_final: 0.3670 (m-10) REVERT: E 199 ASN cc_start: 0.7258 (p0) cc_final: 0.6996 (p0) REVERT: G 99 GLU cc_start: 0.7566 (tp30) cc_final: 0.7318 (tp30) REVERT: H 37 ILE cc_start: 0.8645 (mm) cc_final: 0.8427 (tp) REVERT: H 79 PHE cc_start: 0.8336 (t80) cc_final: 0.8004 (t80) REVERT: H 112 MET cc_start: 0.7230 (ptp) cc_final: 0.6324 (ptp) REVERT: H 190 MET cc_start: 0.8753 (mtt) cc_final: 0.8519 (mtm) REVERT: H 226 ASN cc_start: 0.6402 (p0) cc_final: 0.6179 (p0) REVERT: H 254 TYR cc_start: 0.8328 (t80) cc_final: 0.7800 (t80) REVERT: H 300 MET cc_start: 0.7514 (ttt) cc_final: 0.7214 (ttp) REVERT: H 388 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.6655 (p0) REVERT: H 422 TYR cc_start: 0.8620 (p90) cc_final: 0.7940 (p90) REVERT: H 454 MET cc_start: 0.6886 (mmp) cc_final: 0.6425 (tmm) REVERT: X 130 MET cc_start: 0.8356 (tmm) cc_final: 0.7961 (ppp) REVERT: X 216 VAL cc_start: 0.8637 (m) cc_final: 0.8111 (t) REVERT: X 310 SER cc_start: 0.9420 (p) cc_final: 0.9167 (p) REVERT: X 379 MET cc_start: 0.7397 (mmt) cc_final: 0.7110 (mmt) REVERT: X 591 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7671 (ttt90) REVERT: J 57 TYR cc_start: 0.8970 (p90) cc_final: 0.8705 (p90) REVERT: K 50 ASN cc_start: 0.7836 (p0) cc_final: 0.7504 (p0) REVERT: K 131 MET cc_start: 0.7494 (ttm) cc_final: 0.7243 (ttm) REVERT: K 145 HIS cc_start: 0.7711 (m-70) cc_final: 0.7375 (m170) REVERT: L 26 TYR cc_start: 0.8932 (p90) cc_final: 0.8459 (p90) REVERT: L 33 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8876 (tm-30) REVERT: L 93 GLU cc_start: 0.8179 (pt0) cc_final: 0.7346 (pt0) REVERT: L 96 TYR cc_start: 0.8993 (t80) cc_final: 0.8694 (t80) REVERT: L 133 MET cc_start: 0.8228 (tmm) cc_final: 0.7756 (tmm) REVERT: L 160 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7512 (tm-30) REVERT: L 282 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7830 (mm-30) REVERT: M 35 ARG cc_start: 0.8577 (mtt-85) cc_final: 0.8254 (mtp85) REVERT: M 103 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8376 (mp) REVERT: M 209 MET cc_start: 0.8027 (pmm) cc_final: 0.7755 (pmm) REVERT: M 290 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8149 (tptt) REVERT: M 295 TRP cc_start: 0.8290 (m100) cc_final: 0.8035 (m100) REVERT: N 74 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8429 (tpt90) REVERT: N 132 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6890 (t70) REVERT: a 78 MET cc_start: 0.8187 (mpp) cc_final: 0.7894 (mtm) REVERT: a 91 HIS cc_start: 0.4483 (OUTLIER) cc_final: 0.4154 (t-170) REVERT: b 49 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6843 (m-10) REVERT: b 67 ILE cc_start: 0.7773 (mt) cc_final: 0.7412 (tp) REVERT: c 19 TYR cc_start: 0.7056 (m-80) cc_final: 0.6714 (m-80) REVERT: c 36 MET cc_start: 0.8826 (ppp) cc_final: 0.8357 (ppp) REVERT: d 8 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: d 70 PHE cc_start: 0.7773 (t80) cc_final: 0.7247 (t80) REVERT: e 108 LEU cc_start: 0.8441 (tt) cc_final: 0.8211 (tp) REVERT: e 145 MET cc_start: 0.7580 (tpt) cc_final: 0.7127 (tpt) REVERT: e 168 MET cc_start: 0.5607 (mtt) cc_final: 0.5058 (mtp) REVERT: e 219 LYS cc_start: 0.9058 (tttp) cc_final: 0.8750 (ttpp) REVERT: e 229 ASP cc_start: 0.6708 (m-30) cc_final: 0.6357 (m-30) REVERT: g 41 ASN cc_start: 0.9118 (p0) cc_final: 0.8873 (p0) REVERT: g 100 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8630 (mmtt) REVERT: h 18 PHE cc_start: 0.6832 (t80) cc_final: 0.6534 (t80) REVERT: h 37 ILE cc_start: 0.8697 (mm) cc_final: 0.8489 (tp) REVERT: h 79 PHE cc_start: 0.8278 (t80) cc_final: 0.8015 (t80) REVERT: h 112 MET cc_start: 0.7043 (ptp) cc_final: 0.6245 (ptp) REVERT: h 158 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8407 (tm-30) REVERT: h 254 TYR cc_start: 0.8305 (t80) cc_final: 0.7812 (t80) REVERT: h 279 MET cc_start: 0.7204 (mmp) cc_final: 0.6636 (mtp) REVERT: h 289 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8841 (tt) REVERT: h 379 ILE cc_start: 0.9074 (mm) cc_final: 0.8856 (mt) REVERT: h 388 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.6826 (p0) REVERT: h 422 TYR cc_start: 0.8677 (p90) cc_final: 0.7890 (p90) REVERT: h 454 MET cc_start: 0.6667 (mmp) cc_final: 0.6248 (ppp) REVERT: h 467 TRP cc_start: 0.8640 (t-100) cc_final: 0.8262 (t-100) REVERT: x 130 MET cc_start: 0.8336 (tmm) cc_final: 0.7942 (ppp) REVERT: x 216 VAL cc_start: 0.8635 (m) cc_final: 0.8119 (t) REVERT: x 300 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8665 (tp-100) REVERT: x 305 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8179 (ttpp) REVERT: x 310 SER cc_start: 0.9424 (p) cc_final: 0.9144 (p) REVERT: x 373 MET cc_start: 0.7666 (ptp) cc_final: 0.7371 (ptp) REVERT: x 434 TYR cc_start: 0.7642 (t80) cc_final: 0.7249 (t80) REVERT: x 591 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7671 (ttt90) REVERT: j 128 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8095 (mm-30) REVERT: k 145 HIS cc_start: 0.7736 (m-70) cc_final: 0.7390 (m170) REVERT: l 33 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8854 (tm-30) REVERT: l 82 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9237 (mm) REVERT: l 133 MET cc_start: 0.8230 (tmm) cc_final: 0.8003 (tmm) REVERT: l 187 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8878 (mm) REVERT: m 21 ILE cc_start: 0.9295 (mm) cc_final: 0.8884 (mt) REVERT: m 69 ILE cc_start: 0.8638 (mm) cc_final: 0.8363 (tp) REVERT: m 103 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8348 (mp) REVERT: m 158 GLU cc_start: 0.8090 (mp0) cc_final: 0.7862 (mm-30) REVERT: m 186 LEU cc_start: 0.9019 (mt) cc_final: 0.8759 (tt) REVERT: m 271 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8339 (mp) REVERT: m 290 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8172 (tptt) REVERT: n 27 LEU cc_start: 0.9390 (tp) cc_final: 0.9163 (tp) REVERT: n 74 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8405 (tpt90) REVERT: n 92 ASP cc_start: 0.8295 (p0) cc_final: 0.8009 (p0) REVERT: n 93 TYR cc_start: 0.9094 (m-80) cc_final: 0.8399 (m-80) REVERT: n 132 ASP cc_start: 0.7702 (t0) cc_final: 0.6902 (t70) outliers start: 285 outliers final: 178 residues processed: 1201 average time/residue: 0.4518 time to fit residues: 945.6497 Evaluate side-chains 1143 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 946 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 66 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 506 LEU Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 591 ARG Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 122 MET Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 273 LEU Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain M residue 212 PHE Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain M residue 297 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 70 PHE Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 8 GLU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 312 ILE Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 388 ASN Chi-restraints excluded: chain h residue 430 MET Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain h residue 480 VAL Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain x residue 579 ILE Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 114 ILE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 154 GLU Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 187 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 79 THR Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 486 optimal weight: 4.9990 chunk 331 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 434 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 498 optimal weight: 0.9980 chunk 403 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 298 optimal weight: 0.0470 chunk 524 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN G 73 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 321 GLN X 340 HIS L 39 ASN L 113 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 321 GLN ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN l 113 GLN ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 237 ASN ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 49624 Z= 0.219 Angle : 0.730 14.213 67458 Z= 0.363 Chirality : 0.043 0.225 7768 Planarity : 0.005 0.071 8248 Dihedral : 6.034 59.674 6667 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.70 % Favored : 89.23 % Rotamer: Outliers : 5.56 % Allowed : 24.96 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.10), residues: 6072 helix: -0.54 (0.09), residues: 3484 sheet: -3.26 (0.30), residues: 248 loop : -3.72 (0.11), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 20 HIS 0.004 0.001 HIS x 340 PHE 0.026 0.001 PHE M 112 TYR 0.031 0.002 TYR G 5 ARG 0.010 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1043 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7615 (t-100) cc_final: 0.7345 (t60) REVERT: A 78 MET cc_start: 0.8244 (mpp) cc_final: 0.7772 (mtt) REVERT: A 83 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7130 (mm) REVERT: A 114 MET cc_start: 0.7621 (mtt) cc_final: 0.7133 (mtp) REVERT: B 67 ILE cc_start: 0.7844 (mp) cc_final: 0.7326 (tp) REVERT: C 35 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7589 (ttm110) REVERT: D 70 PHE cc_start: 0.7666 (t80) cc_final: 0.7397 (t80) REVERT: E 120 ILE cc_start: 0.8372 (mm) cc_final: 0.8001 (mt) REVERT: E 145 MET cc_start: 0.7905 (tpt) cc_final: 0.7634 (tpp) REVERT: E 146 TYR cc_start: 0.7788 (t80) cc_final: 0.6902 (t80) REVERT: E 193 TRP cc_start: 0.4140 (p-90) cc_final: 0.3658 (m-10) REVERT: E 199 ASN cc_start: 0.7170 (p0) cc_final: 0.6934 (p0) REVERT: G 99 GLU cc_start: 0.7459 (tp30) cc_final: 0.7232 (tp30) REVERT: H 37 ILE cc_start: 0.8618 (mm) cc_final: 0.8330 (tp) REVERT: H 79 PHE cc_start: 0.8233 (t80) cc_final: 0.7929 (t80) REVERT: H 96 LEU cc_start: 0.7920 (pp) cc_final: 0.7472 (tp) REVERT: H 112 MET cc_start: 0.7198 (ptp) cc_final: 0.6304 (ptp) REVERT: H 254 TYR cc_start: 0.8293 (t80) cc_final: 0.7818 (t80) REVERT: H 300 MET cc_start: 0.7514 (ttt) cc_final: 0.7237 (ttp) REVERT: H 388 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.6602 (p0) REVERT: H 422 TYR cc_start: 0.8562 (p90) cc_final: 0.7912 (p90) REVERT: H 454 MET cc_start: 0.6734 (mmp) cc_final: 0.6404 (tmm) REVERT: X 13 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7383 (tt) REVERT: X 130 MET cc_start: 0.8382 (tmm) cc_final: 0.8025 (ppp) REVERT: X 310 SER cc_start: 0.9403 (p) cc_final: 0.9173 (p) REVERT: X 379 MET cc_start: 0.7338 (mmt) cc_final: 0.6818 (mmt) REVERT: X 434 TYR cc_start: 0.7465 (t80) cc_final: 0.7206 (t80) REVERT: X 591 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7654 (ttt90) REVERT: J 57 TYR cc_start: 0.8952 (p90) cc_final: 0.8643 (p90) REVERT: J 128 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8205 (mm-30) REVERT: K 44 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6169 (ptp-110) REVERT: K 50 ASN cc_start: 0.7781 (p0) cc_final: 0.7458 (p0) REVERT: K 69 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7556 (mt-10) REVERT: K 145 HIS cc_start: 0.7692 (m-70) cc_final: 0.7349 (m170) REVERT: L 26 TYR cc_start: 0.8848 (p90) cc_final: 0.8460 (p90) REVERT: L 33 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8872 (tm-30) REVERT: L 93 GLU cc_start: 0.8170 (pt0) cc_final: 0.7307 (pt0) REVERT: L 96 TYR cc_start: 0.8965 (t80) cc_final: 0.8684 (t80) REVERT: L 133 MET cc_start: 0.8194 (tmm) cc_final: 0.7734 (tmm) REVERT: L 160 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7413 (tm-30) REVERT: L 282 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7861 (mm-30) REVERT: L 368 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8287 (m) REVERT: M 21 ILE cc_start: 0.9267 (mm) cc_final: 0.8849 (mt) REVERT: M 35 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.8258 (mtp85) REVERT: M 103 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8450 (mp) REVERT: M 104 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7140 (mt-10) REVERT: M 137 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7882 (mm-40) REVERT: M 158 GLU cc_start: 0.8198 (mp0) cc_final: 0.7849 (mm-30) REVERT: M 290 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8164 (tptt) REVERT: M 295 TRP cc_start: 0.8180 (m100) cc_final: 0.7970 (m100) REVERT: N 132 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6842 (t70) REVERT: a 66 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.6096 (m-80) REVERT: a 83 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6853 (mm) REVERT: a 91 HIS cc_start: 0.4458 (t-90) cc_final: 0.4144 (t-170) REVERT: a 114 MET cc_start: 0.7642 (mtm) cc_final: 0.7296 (mtp) REVERT: b 67 ILE cc_start: 0.7733 (mt) cc_final: 0.7361 (tp) REVERT: c 19 TYR cc_start: 0.7097 (m-80) cc_final: 0.6655 (m-80) REVERT: c 36 MET cc_start: 0.8743 (ppp) cc_final: 0.8315 (ppp) REVERT: d 70 PHE cc_start: 0.7655 (t80) cc_final: 0.7207 (t80) REVERT: e 120 ILE cc_start: 0.8636 (mm) cc_final: 0.8311 (mt) REVERT: e 168 MET cc_start: 0.5699 (mtt) cc_final: 0.5129 (mtp) REVERT: e 219 LYS cc_start: 0.9036 (tttp) cc_final: 0.8735 (ttpp) REVERT: e 229 ASP cc_start: 0.6572 (m-30) cc_final: 0.6234 (m-30) REVERT: g 24 LYS cc_start: 0.8094 (mttp) cc_final: 0.7887 (mmtp) REVERT: g 41 ASN cc_start: 0.9105 (p0) cc_final: 0.8862 (p0) REVERT: g 100 LYS cc_start: 0.8785 (mmtm) cc_final: 0.8573 (mmtt) REVERT: h 18 PHE cc_start: 0.6725 (t80) cc_final: 0.6468 (t80) REVERT: h 79 PHE cc_start: 0.8190 (t80) cc_final: 0.7868 (t80) REVERT: h 96 LEU cc_start: 0.7999 (pp) cc_final: 0.7394 (tp) REVERT: h 112 MET cc_start: 0.7023 (ptp) cc_final: 0.6253 (ptp) REVERT: h 134 PHE cc_start: 0.8624 (t80) cc_final: 0.8130 (t80) REVERT: h 158 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8407 (tm-30) REVERT: h 240 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8985 (tp) REVERT: h 254 TYR cc_start: 0.8287 (t80) cc_final: 0.7864 (t80) REVERT: h 289 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8799 (tt) REVERT: h 379 ILE cc_start: 0.9096 (mm) cc_final: 0.8885 (mt) REVERT: h 388 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.6721 (p0) REVERT: h 422 TYR cc_start: 0.8586 (p90) cc_final: 0.7835 (p90) REVERT: h 454 MET cc_start: 0.6538 (mmp) cc_final: 0.6296 (tmm) REVERT: x 13 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7499 (tt) REVERT: x 120 PHE cc_start: 0.7420 (t80) cc_final: 0.6769 (t80) REVERT: x 130 MET cc_start: 0.8416 (tmm) cc_final: 0.8089 (ppp) REVERT: x 300 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8624 (tp-100) REVERT: x 305 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8079 (ttpp) REVERT: x 310 SER cc_start: 0.9408 (p) cc_final: 0.9091 (p) REVERT: x 379 MET cc_start: 0.7605 (mmt) cc_final: 0.7313 (mmt) REVERT: x 434 TYR cc_start: 0.7558 (t80) cc_final: 0.7182 (t80) REVERT: x 591 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7568 (ttt90) REVERT: j 57 TYR cc_start: 0.8869 (p90) cc_final: 0.8581 (p90) REVERT: j 128 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8061 (mm-30) REVERT: k 145 HIS cc_start: 0.7711 (m-70) cc_final: 0.7218 (m-70) REVERT: l 33 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8841 (tm-30) REVERT: l 81 LEU cc_start: 0.8991 (tp) cc_final: 0.8614 (tt) REVERT: l 82 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9250 (mm) REVERT: l 133 MET cc_start: 0.8305 (tmm) cc_final: 0.7840 (tmm) REVERT: l 187 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8875 (mm) REVERT: l 282 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7906 (mm-30) REVERT: m 21 ILE cc_start: 0.9279 (mm) cc_final: 0.8867 (mt) REVERT: m 103 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8301 (mp) REVERT: m 186 LEU cc_start: 0.9058 (mt) cc_final: 0.8821 (tt) REVERT: m 209 MET cc_start: 0.8446 (pmm) cc_final: 0.8213 (pmm) REVERT: m 274 ILE cc_start: 0.8768 (mm) cc_final: 0.8377 (tp) REVERT: m 290 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8206 (tptt) REVERT: n 74 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8246 (tpt90) REVERT: n 92 ASP cc_start: 0.8261 (p0) cc_final: 0.8001 (p0) REVERT: n 93 TYR cc_start: 0.9075 (m-80) cc_final: 0.8208 (m-10) REVERT: n 132 ASP cc_start: 0.7530 (t0) cc_final: 0.6837 (t70) outliers start: 280 outliers final: 164 residues processed: 1238 average time/residue: 0.5012 time to fit residues: 1082.5684 Evaluate side-chains 1143 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 959 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 321 GLN Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 591 ARG Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 610 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 292 GLN Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain L residue 368 VAL Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 73 GLN Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 321 GLN Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 388 ASN Chi-restraints excluded: chain h residue 430 MET Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 340 HIS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 548 TYR Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 114 ASP Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 172 THR Chi-restraints excluded: chain l residue 187 LEU Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 234 VAL Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 273 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 155 SER Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain m residue 212 PHE Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 196 optimal weight: 0.9980 chunk 525 optimal weight: 0.2980 chunk 115 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 144 optimal weight: 0.0870 chunk 584 optimal weight: 5.9990 chunk 485 optimal weight: 0.7980 chunk 270 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 HIS ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 321 GLN H 359 ASN X 340 HIS L 39 ASN L 384 ASN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 321 GLN ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 127 GLN ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 49624 Z= 0.200 Angle : 0.732 15.155 67458 Z= 0.361 Chirality : 0.044 0.423 7768 Planarity : 0.005 0.093 8248 Dihedral : 5.790 59.630 6659 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.18 % Favored : 89.76 % Rotamer: Outliers : 5.08 % Allowed : 26.63 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 6072 helix: -0.39 (0.09), residues: 3500 sheet: -3.17 (0.29), residues: 248 loop : -3.65 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 21 HIS 0.004 0.001 HIS x 340 PHE 0.026 0.001 PHE M 112 TYR 0.025 0.001 TYR c 94 ARG 0.011 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1036 time to evaluate : 4.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7615 (t-100) cc_final: 0.7344 (t60) REVERT: A 78 MET cc_start: 0.8208 (mpp) cc_final: 0.7845 (mtt) REVERT: A 83 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7025 (mm) REVERT: D 38 VAL cc_start: 0.8608 (t) cc_final: 0.8339 (p) REVERT: E 120 ILE cc_start: 0.8399 (mm) cc_final: 0.7999 (mt) REVERT: E 145 MET cc_start: 0.7816 (tpt) cc_final: 0.7588 (tpp) REVERT: E 146 TYR cc_start: 0.7666 (t80) cc_final: 0.6733 (t80) REVERT: E 193 TRP cc_start: 0.4172 (p-90) cc_final: 0.3587 (m-10) REVERT: E 223 GLU cc_start: 0.7274 (tp30) cc_final: 0.6925 (tp30) REVERT: G 7 PHE cc_start: 0.7482 (t80) cc_final: 0.7071 (t80) REVERT: G 37 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7528 (tm-30) REVERT: G 99 GLU cc_start: 0.7411 (tp30) cc_final: 0.7211 (tp30) REVERT: H 37 ILE cc_start: 0.8673 (mm) cc_final: 0.8403 (tp) REVERT: H 79 PHE cc_start: 0.8159 (t80) cc_final: 0.7860 (t80) REVERT: H 96 LEU cc_start: 0.7893 (pp) cc_final: 0.7469 (tp) REVERT: H 112 MET cc_start: 0.7146 (ptp) cc_final: 0.6267 (ptp) REVERT: H 134 PHE cc_start: 0.8699 (t80) cc_final: 0.8407 (t80) REVERT: H 254 TYR cc_start: 0.8211 (t80) cc_final: 0.7684 (t80) REVERT: H 388 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.6556 (p0) REVERT: H 422 TYR cc_start: 0.8505 (p90) cc_final: 0.7906 (p90) REVERT: H 454 MET cc_start: 0.6620 (mmp) cc_final: 0.6385 (ppp) REVERT: X 13 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7440 (tt) REVERT: X 130 MET cc_start: 0.8430 (tmm) cc_final: 0.8129 (ppp) REVERT: X 310 SER cc_start: 0.9396 (OUTLIER) cc_final: 0.9079 (p) REVERT: X 379 MET cc_start: 0.7319 (mmt) cc_final: 0.6801 (mmt) REVERT: X 459 MET cc_start: 0.8553 (mtm) cc_final: 0.8249 (mtm) REVERT: X 591 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7572 (ttt90) REVERT: J 57 TYR cc_start: 0.8925 (p90) cc_final: 0.8644 (p90) REVERT: J 128 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8167 (mm-30) REVERT: K 44 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.6105 (ptp-110) REVERT: K 50 ASN cc_start: 0.7756 (p0) cc_final: 0.7528 (p0) REVERT: K 145 HIS cc_start: 0.7614 (m-70) cc_final: 0.7327 (m170) REVERT: L 26 TYR cc_start: 0.8804 (p90) cc_final: 0.8454 (p90) REVERT: L 33 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8825 (tm-30) REVERT: L 93 GLU cc_start: 0.8151 (pt0) cc_final: 0.7280 (pt0) REVERT: L 96 TYR cc_start: 0.8916 (t80) cc_final: 0.8649 (t80) REVERT: L 133 MET cc_start: 0.8198 (tmm) cc_final: 0.7703 (tmm) REVERT: L 160 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7414 (tm-30) REVERT: M 21 ILE cc_start: 0.9244 (mm) cc_final: 0.8844 (mt) REVERT: M 35 ARG cc_start: 0.8514 (mtt-85) cc_final: 0.8262 (mtp85) REVERT: M 103 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8450 (mp) REVERT: M 104 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6941 (mt-10) REVERT: M 133 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8626 (tp) REVERT: M 137 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7837 (mm-40) REVERT: M 158 GLU cc_start: 0.8259 (mp0) cc_final: 0.8054 (mp0) REVERT: M 290 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8155 (tptt) REVERT: N 27 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9222 (tt) REVERT: N 74 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8418 (tpt90) REVERT: N 132 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6652 (t0) REVERT: a 66 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6201 (m-80) REVERT: a 78 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7860 (mtt) REVERT: a 91 HIS cc_start: 0.4336 (OUTLIER) cc_final: 0.4064 (t-170) REVERT: a 114 MET cc_start: 0.7622 (mtm) cc_final: 0.7322 (mtp) REVERT: b 49 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6706 (m-10) REVERT: b 67 ILE cc_start: 0.7799 (mt) cc_final: 0.7428 (tp) REVERT: c 18 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6556 (t80) REVERT: c 19 TYR cc_start: 0.7170 (m-80) cc_final: 0.6748 (m-80) REVERT: c 21 LEU cc_start: 0.8338 (mm) cc_final: 0.7927 (tt) REVERT: c 36 MET cc_start: 0.8701 (ppp) cc_final: 0.8365 (ppp) REVERT: d 8 GLU cc_start: 0.8125 (tt0) cc_final: 0.7454 (tt0) REVERT: d 14 LEU cc_start: 0.8890 (tp) cc_final: 0.8645 (tp) REVERT: e 120 ILE cc_start: 0.8628 (mm) cc_final: 0.8355 (mt) REVERT: e 146 TYR cc_start: 0.8017 (t80) cc_final: 0.7802 (t80) REVERT: e 168 MET cc_start: 0.5608 (mtt) cc_final: 0.5130 (mtp) REVERT: e 219 LYS cc_start: 0.8991 (tttp) cc_final: 0.8729 (ttpp) REVERT: e 229 ASP cc_start: 0.6417 (m-30) cc_final: 0.6141 (m-30) REVERT: g 24 LYS cc_start: 0.8046 (mttp) cc_final: 0.7542 (pttm) REVERT: g 100 LYS cc_start: 0.8849 (mmtm) cc_final: 0.8605 (mmtt) REVERT: h 18 PHE cc_start: 0.6614 (t80) cc_final: 0.6406 (t80) REVERT: h 96 LEU cc_start: 0.7877 (pp) cc_final: 0.7333 (tp) REVERT: h 112 MET cc_start: 0.7100 (ptp) cc_final: 0.6254 (ptp) REVERT: h 158 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8338 (tm-30) REVERT: h 240 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8890 (tp) REVERT: h 254 TYR cc_start: 0.8122 (t80) cc_final: 0.7693 (t80) REVERT: h 279 MET cc_start: 0.7096 (mmp) cc_final: 0.6652 (mtp) REVERT: h 289 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8804 (tt) REVERT: h 379 ILE cc_start: 0.9086 (mm) cc_final: 0.8875 (mt) REVERT: h 407 TRP cc_start: 0.8052 (m100) cc_final: 0.7771 (m100) REVERT: h 422 TYR cc_start: 0.8597 (p90) cc_final: 0.7878 (p90) REVERT: x 120 PHE cc_start: 0.7419 (t80) cc_final: 0.6732 (t80) REVERT: x 130 MET cc_start: 0.8470 (tmm) cc_final: 0.8135 (ppp) REVERT: x 300 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8571 (tp-100) REVERT: x 305 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8079 (ttpp) REVERT: x 310 SER cc_start: 0.9402 (p) cc_final: 0.9061 (p) REVERT: x 373 MET cc_start: 0.7637 (ptp) cc_final: 0.7334 (ptp) REVERT: x 434 TYR cc_start: 0.7502 (t80) cc_final: 0.7101 (t80) REVERT: x 591 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7592 (ttt90) REVERT: j 57 TYR cc_start: 0.8865 (p90) cc_final: 0.8550 (p90) REVERT: k 145 HIS cc_start: 0.7607 (m-70) cc_final: 0.7342 (m170) REVERT: l 33 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8810 (tm-30) REVERT: l 81 LEU cc_start: 0.8895 (tp) cc_final: 0.8551 (tt) REVERT: l 133 MET cc_start: 0.8293 (tmm) cc_final: 0.7829 (tmm) REVERT: l 166 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7441 (mtp85) REVERT: l 282 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7902 (mm-30) REVERT: l 368 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8199 (m) REVERT: m 21 ILE cc_start: 0.9241 (mm) cc_final: 0.8864 (mt) REVERT: m 103 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8246 (mp) REVERT: m 186 LEU cc_start: 0.9038 (mt) cc_final: 0.8824 (tt) REVERT: m 209 MET cc_start: 0.8402 (pmm) cc_final: 0.7972 (ppp) REVERT: m 274 ILE cc_start: 0.8662 (mm) cc_final: 0.8335 (tp) REVERT: m 290 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8208 (tptt) REVERT: n 74 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8575 (tpt90) REVERT: n 92 ASP cc_start: 0.8235 (p0) cc_final: 0.7878 (p0) REVERT: n 93 TYR cc_start: 0.9008 (m-80) cc_final: 0.8202 (m-10) REVERT: n 132 ASP cc_start: 0.7484 (t0) cc_final: 0.6790 (t70) outliers start: 256 outliers final: 165 residues processed: 1209 average time/residue: 0.4505 time to fit residues: 934.0440 Evaluate side-chains 1149 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 961 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 310 SER Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 382 VAL Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 591 ARG Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain L residue 356 ILE Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 212 PHE Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 132 ASP Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 78 MET Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 49 PHE Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 18 PHE Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 123 HIS Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 115 LEU Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain h residue 247 PHE Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 372 LEU Chi-restraints excluded: chain h residue 430 MET Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 79 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 468 ILE Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 548 TYR Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 114 ASP Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 172 THR Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 255 LEU Chi-restraints excluded: chain l residue 292 GLN Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 368 VAL Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 212 PHE Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 44 ILE Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 563 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 332 optimal weight: 10.0000 chunk 426 optimal weight: 3.9990 chunk 330 optimal weight: 0.9980 chunk 491 optimal weight: 0.7980 chunk 326 optimal weight: 3.9990 chunk 582 optimal weight: 1.9990 chunk 364 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 340 HIS L 39 ASN L 113 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN a 139 HIS ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 132 ASN ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN l 326 HIS ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 49624 Z= 0.246 Angle : 0.751 15.399 67458 Z= 0.371 Chirality : 0.045 0.302 7768 Planarity : 0.005 0.078 8248 Dihedral : 5.691 59.981 6657 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.84 % Favored : 89.11 % Rotamer: Outliers : 5.34 % Allowed : 27.18 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.11), residues: 6072 helix: -0.30 (0.09), residues: 3494 sheet: -3.19 (0.29), residues: 248 loop : -3.60 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 391 HIS 0.010 0.001 HIS l 326 PHE 0.038 0.002 PHE d 47 TYR 0.031 0.002 TYR M 157 ARG 0.012 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 985 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7701 (t-100) cc_final: 0.7420 (t60) REVERT: A 78 MET cc_start: 0.8213 (mpp) cc_final: 0.8000 (mtt) REVERT: A 83 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7080 (mm) REVERT: B 67 ILE cc_start: 0.7602 (mp) cc_final: 0.7249 (tp) REVERT: D 38 VAL cc_start: 0.8626 (t) cc_final: 0.8383 (p) REVERT: D 70 PHE cc_start: 0.7675 (t80) cc_final: 0.7473 (t80) REVERT: E 120 ILE cc_start: 0.8372 (mm) cc_final: 0.7972 (mt) REVERT: E 145 MET cc_start: 0.7849 (tpt) cc_final: 0.7596 (tpp) REVERT: E 193 TRP cc_start: 0.4112 (p-90) cc_final: 0.3684 (m-10) REVERT: G 7 PHE cc_start: 0.7450 (t80) cc_final: 0.6950 (t80) REVERT: G 37 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7589 (tm-30) REVERT: H 27 LYS cc_start: 0.3999 (tptp) cc_final: 0.3755 (tptp) REVERT: H 37 ILE cc_start: 0.8630 (mm) cc_final: 0.8348 (tp) REVERT: H 79 PHE cc_start: 0.8189 (t80) cc_final: 0.7922 (t80) REVERT: H 96 LEU cc_start: 0.7899 (pp) cc_final: 0.7482 (tp) REVERT: H 112 MET cc_start: 0.7196 (ptp) cc_final: 0.6287 (ptp) REVERT: H 254 TYR cc_start: 0.8250 (t80) cc_final: 0.7770 (t80) REVERT: H 388 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.6616 (p0) REVERT: X 13 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7486 (tt) REVERT: X 130 MET cc_start: 0.8471 (tmm) cc_final: 0.8250 (ppp) REVERT: X 261 MET cc_start: 0.7787 (pmm) cc_final: 0.7569 (pmm) REVERT: X 305 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8255 (ttpp) REVERT: X 310 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9099 (p) REVERT: X 379 MET cc_start: 0.7306 (mmt) cc_final: 0.6797 (mmt) REVERT: X 434 TYR cc_start: 0.7761 (t80) cc_final: 0.7398 (t80) REVERT: X 459 MET cc_start: 0.8518 (mtm) cc_final: 0.8243 (mtm) REVERT: X 591 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7659 (ttt90) REVERT: J 57 TYR cc_start: 0.9007 (p90) cc_final: 0.8710 (p90) REVERT: J 128 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8224 (mm-30) REVERT: K 44 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.6169 (ptp-110) REVERT: K 50 ASN cc_start: 0.7863 (p0) cc_final: 0.7620 (p0) REVERT: L 26 TYR cc_start: 0.8776 (p90) cc_final: 0.8529 (p90) REVERT: L 33 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8878 (tm-30) REVERT: L 93 GLU cc_start: 0.8202 (pt0) cc_final: 0.7298 (pt0) REVERT: L 96 TYR cc_start: 0.8926 (t80) cc_final: 0.8705 (t80) REVERT: L 133 MET cc_start: 0.8192 (tmm) cc_final: 0.7746 (tmm) REVERT: L 160 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7456 (tm-30) REVERT: M 21 ILE cc_start: 0.9265 (mm) cc_final: 0.8865 (mt) REVERT: M 35 ARG cc_start: 0.8544 (mtt-85) cc_final: 0.8246 (mtp85) REVERT: M 103 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8491 (mp) REVERT: M 137 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7897 (mm-40) REVERT: M 209 MET cc_start: 0.8286 (pmm) cc_final: 0.7862 (ppp) REVERT: M 290 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8171 (tptt) REVERT: N 43 PHE cc_start: 0.7214 (t80) cc_final: 0.6803 (t80) REVERT: N 74 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8649 (tpt90) REVERT: N 132 ASP cc_start: 0.7312 (t0) cc_final: 0.6854 (t70) REVERT: a 66 TYR cc_start: 0.6907 (OUTLIER) cc_final: 0.6303 (m-80) REVERT: a 78 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: a 83 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6862 (mm) REVERT: a 91 HIS cc_start: 0.4298 (OUTLIER) cc_final: 0.4021 (t-170) REVERT: a 114 MET cc_start: 0.7652 (mtm) cc_final: 0.7320 (mtp) REVERT: c 21 LEU cc_start: 0.8317 (mm) cc_final: 0.7896 (tt) REVERT: c 36 MET cc_start: 0.8639 (ppp) cc_final: 0.8333 (ppp) REVERT: c 56 ILE cc_start: 0.6628 (pt) cc_final: 0.6421 (mm) REVERT: d 14 LEU cc_start: 0.8938 (tp) cc_final: 0.8731 (tp) REVERT: e 66 ASP cc_start: 0.7310 (m-30) cc_final: 0.6879 (t70) REVERT: e 120 ILE cc_start: 0.8641 (mm) cc_final: 0.8358 (mt) REVERT: e 146 TYR cc_start: 0.8060 (t80) cc_final: 0.7816 (t80) REVERT: e 168 MET cc_start: 0.5666 (mtt) cc_final: 0.5157 (mtp) REVERT: e 219 LYS cc_start: 0.9010 (tttp) cc_final: 0.8690 (ttpp) REVERT: e 229 ASP cc_start: 0.6241 (m-30) cc_final: 0.5935 (m-30) REVERT: g 37 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7575 (tm-30) REVERT: g 100 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8635 (mmtt) REVERT: h 18 PHE cc_start: 0.6686 (t80) cc_final: 0.6476 (t80) REVERT: h 96 LEU cc_start: 0.7857 (pp) cc_final: 0.7274 (tp) REVERT: h 112 MET cc_start: 0.7097 (ptp) cc_final: 0.6316 (ptp) REVERT: h 134 PHE cc_start: 0.8466 (t80) cc_final: 0.8077 (t80) REVERT: h 158 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8335 (tm-30) REVERT: h 240 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8913 (tp) REVERT: h 254 TYR cc_start: 0.8117 (t80) cc_final: 0.7670 (t80) REVERT: h 279 MET cc_start: 0.7096 (mmp) cc_final: 0.6615 (mtp) REVERT: h 289 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8857 (tt) REVERT: h 379 ILE cc_start: 0.9106 (mm) cc_final: 0.8882 (mt) REVERT: x 13 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7501 (tt) REVERT: x 120 PHE cc_start: 0.7486 (t80) cc_final: 0.6805 (t80) REVERT: x 130 MET cc_start: 0.8483 (tmm) cc_final: 0.8127 (ppp) REVERT: x 300 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8572 (tp-100) REVERT: x 305 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8143 (ttpp) REVERT: x 310 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9099 (p) REVERT: x 373 MET cc_start: 0.7684 (ptp) cc_final: 0.7423 (ptp) REVERT: x 434 TYR cc_start: 0.7451 (t80) cc_final: 0.7123 (t80) REVERT: x 591 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7585 (ttt90) REVERT: j 57 TYR cc_start: 0.8921 (p90) cc_final: 0.8602 (p90) REVERT: k 62 TRP cc_start: 0.8545 (m100) cc_final: 0.8272 (m100) REVERT: k 98 MET cc_start: 0.8348 (tpp) cc_final: 0.8112 (tpp) REVERT: k 145 HIS cc_start: 0.7655 (m-70) cc_final: 0.7363 (m170) REVERT: l 33 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8877 (tm-30) REVERT: l 81 LEU cc_start: 0.8975 (tp) cc_final: 0.8606 (tt) REVERT: l 93 GLU cc_start: 0.8210 (pt0) cc_final: 0.7160 (pt0) REVERT: l 133 MET cc_start: 0.8256 (tmm) cc_final: 0.7850 (tmm) REVERT: l 282 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7925 (mm-30) REVERT: l 368 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8284 (m) REVERT: m 21 ILE cc_start: 0.9269 (mm) cc_final: 0.8864 (mt) REVERT: m 103 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8302 (mp) REVERT: m 209 MET cc_start: 0.8390 (pmm) cc_final: 0.8164 (pmm) REVERT: m 274 ILE cc_start: 0.8664 (mm) cc_final: 0.8305 (tp) REVERT: m 290 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8234 (tptt) REVERT: n 74 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8579 (tpt90) REVERT: n 92 ASP cc_start: 0.8196 (p0) cc_final: 0.7889 (p0) REVERT: n 93 TYR cc_start: 0.9087 (m-80) cc_final: 0.8486 (m-80) REVERT: n 132 ASP cc_start: 0.7613 (t0) cc_final: 0.6847 (t70) outliers start: 269 outliers final: 190 residues processed: 1175 average time/residue: 0.4538 time to fit residues: 914.2653 Evaluate side-chains 1164 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 953 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 310 SER Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 548 TYR Chi-restraints excluded: chain X residue 591 ARG Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 197 LEU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain L residue 356 ILE Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 154 PHE Chi-restraints excluded: chain M residue 155 SER Chi-restraints excluded: chain M residue 212 PHE Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 78 MET Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 123 HIS Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 231 MET Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 105 ASN Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 115 LEU Chi-restraints excluded: chain h residue 129 ASP Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 430 MET Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 141 TYR Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 310 SER Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 514 ILE Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 548 TYR Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 114 ILE Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 114 ASP Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 167 VAL Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 234 VAL Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 255 LEU Chi-restraints excluded: chain l residue 292 GLN Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 326 HIS Chi-restraints excluded: chain l residue 368 VAL Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 154 PHE Chi-restraints excluded: chain m residue 212 PHE Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 259 LEU Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 20 PHE Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 360 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 347 optimal weight: 0.8980 chunk 175 optimal weight: 0.0670 chunk 114 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 370 optimal weight: 4.9990 chunk 396 optimal weight: 0.8980 chunk 287 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 457 optimal weight: 3.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 ASN X 340 HIS ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN ** M 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 109 GLN ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 49624 Z= 0.209 Angle : 0.751 16.733 67458 Z= 0.368 Chirality : 0.044 0.324 7768 Planarity : 0.005 0.072 8248 Dihedral : 5.620 59.870 6656 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.29 % Favored : 89.66 % Rotamer: Outliers : 4.86 % Allowed : 27.68 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.11), residues: 6072 helix: -0.18 (0.09), residues: 3486 sheet: -3.08 (0.31), residues: 214 loop : -3.55 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP a 21 HIS 0.036 0.001 HIS l 326 PHE 0.030 0.001 PHE C 18 TYR 0.039 0.001 TYR g 5 ARG 0.007 0.000 ARG a 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1003 time to evaluate : 4.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7676 (t-100) cc_final: 0.7425 (t60) REVERT: A 83 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7113 (mm) REVERT: B 67 ILE cc_start: 0.7559 (mp) cc_final: 0.7174 (tp) REVERT: D 38 VAL cc_start: 0.8609 (t) cc_final: 0.8388 (p) REVERT: E 120 ILE cc_start: 0.8366 (mm) cc_final: 0.7959 (mt) REVERT: E 145 MET cc_start: 0.7832 (tpt) cc_final: 0.7532 (tpp) REVERT: E 193 TRP cc_start: 0.4204 (p-90) cc_final: 0.3628 (m-10) REVERT: G 7 PHE cc_start: 0.7400 (t80) cc_final: 0.6979 (t80) REVERT: G 37 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7541 (tm-30) REVERT: H 27 LYS cc_start: 0.4024 (tptp) cc_final: 0.3755 (tptp) REVERT: H 37 ILE cc_start: 0.8591 (mm) cc_final: 0.8342 (tp) REVERT: H 79 PHE cc_start: 0.8095 (t80) cc_final: 0.7873 (t80) REVERT: H 96 LEU cc_start: 0.7792 (pp) cc_final: 0.7393 (tp) REVERT: H 112 MET cc_start: 0.7170 (ptp) cc_final: 0.6244 (ptp) REVERT: H 254 TYR cc_start: 0.8218 (t80) cc_final: 0.7711 (t80) REVERT: H 388 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.6574 (p0) REVERT: X 13 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7487 (tt) REVERT: X 130 MET cc_start: 0.8468 (tmm) cc_final: 0.8159 (ppp) REVERT: X 261 MET cc_start: 0.7730 (pmm) cc_final: 0.7500 (pmm) REVERT: X 305 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8279 (ttpp) REVERT: X 310 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.9065 (p) REVERT: X 379 MET cc_start: 0.7343 (mmt) cc_final: 0.6811 (mmt) REVERT: X 459 MET cc_start: 0.8528 (mtm) cc_final: 0.8280 (mtm) REVERT: X 591 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7566 (ttt90) REVERT: J 57 TYR cc_start: 0.8944 (p90) cc_final: 0.8619 (p90) REVERT: J 128 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8180 (mm-30) REVERT: K 44 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.6052 (ptp-110) REVERT: K 50 ASN cc_start: 0.7902 (p0) cc_final: 0.7654 (p0) REVERT: L 33 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8846 (tm-30) REVERT: L 93 GLU cc_start: 0.8175 (pt0) cc_final: 0.7229 (pt0) REVERT: L 96 TYR cc_start: 0.8907 (t80) cc_final: 0.8702 (t80) REVERT: L 133 MET cc_start: 0.8152 (tmm) cc_final: 0.7698 (tmm) REVERT: L 160 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7410 (tm-30) REVERT: L 189 GLN cc_start: 0.7487 (tp40) cc_final: 0.7282 (tp40) REVERT: M 21 ILE cc_start: 0.9252 (mm) cc_final: 0.8854 (mt) REVERT: M 35 ARG cc_start: 0.8488 (mtt-85) cc_final: 0.8221 (mtp85) REVERT: M 103 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8482 (mp) REVERT: M 104 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7007 (mt-10) REVERT: M 209 MET cc_start: 0.8231 (pmm) cc_final: 0.7796 (ppp) REVERT: M 290 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8164 (tptt) REVERT: N 43 PHE cc_start: 0.7124 (t80) cc_final: 0.6728 (t80) REVERT: N 74 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8670 (tpt90) REVERT: N 132 ASP cc_start: 0.7134 (t0) cc_final: 0.6706 (t70) REVERT: a 66 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.6375 (m-80) REVERT: a 78 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7820 (mpp) REVERT: a 83 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6807 (mm) REVERT: a 91 HIS cc_start: 0.4240 (OUTLIER) cc_final: 0.4012 (t-170) REVERT: a 114 MET cc_start: 0.7570 (mtm) cc_final: 0.7293 (mtp) REVERT: b 67 ILE cc_start: 0.7588 (mt) cc_final: 0.7353 (tp) REVERT: c 21 LEU cc_start: 0.8283 (mm) cc_final: 0.7896 (tt) REVERT: c 36 MET cc_start: 0.8562 (ppp) cc_final: 0.8298 (ppp) REVERT: c 56 ILE cc_start: 0.6615 (pt) cc_final: 0.6394 (mm) REVERT: d 14 LEU cc_start: 0.8975 (tp) cc_final: 0.8756 (tp) REVERT: e 66 ASP cc_start: 0.7247 (m-30) cc_final: 0.6886 (t70) REVERT: e 119 TYR cc_start: 0.8487 (t80) cc_final: 0.8256 (t80) REVERT: e 120 ILE cc_start: 0.8625 (mm) cc_final: 0.8258 (mt) REVERT: e 146 TYR cc_start: 0.8017 (t80) cc_final: 0.7109 (t80) REVERT: e 168 MET cc_start: 0.5595 (mtt) cc_final: 0.5105 (mtp) REVERT: e 219 LYS cc_start: 0.8973 (tttp) cc_final: 0.8202 (tmmt) REVERT: g 37 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7531 (tm-30) REVERT: g 100 LYS cc_start: 0.8870 (mmtm) cc_final: 0.8623 (mmtt) REVERT: h 18 PHE cc_start: 0.6591 (t80) cc_final: 0.6374 (t80) REVERT: h 96 LEU cc_start: 0.7785 (pp) cc_final: 0.7220 (tp) REVERT: h 112 MET cc_start: 0.7084 (ptp) cc_final: 0.6272 (ptp) REVERT: h 158 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8314 (tm-30) REVERT: h 240 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8880 (tp) REVERT: h 254 TYR cc_start: 0.7987 (t80) cc_final: 0.7609 (t80) REVERT: h 279 MET cc_start: 0.7148 (mmp) cc_final: 0.6846 (ttp) REVERT: h 289 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8838 (tt) REVERT: h 379 ILE cc_start: 0.9110 (mm) cc_final: 0.8894 (mt) REVERT: h 407 TRP cc_start: 0.7923 (m100) cc_final: 0.7536 (m100) REVERT: x 13 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7569 (tt) REVERT: x 43 ILE cc_start: 0.8030 (mm) cc_final: 0.7553 (mt) REVERT: x 120 PHE cc_start: 0.7463 (t80) cc_final: 0.6740 (t80) REVERT: x 130 MET cc_start: 0.8484 (tmm) cc_final: 0.8124 (ppp) REVERT: x 300 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8604 (tp-100) REVERT: x 305 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8105 (ttpp) REVERT: x 310 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.9081 (p) REVERT: x 373 MET cc_start: 0.7695 (ptp) cc_final: 0.7423 (ptp) REVERT: x 379 MET cc_start: 0.7651 (mmt) cc_final: 0.7165 (mmt) REVERT: x 434 TYR cc_start: 0.7368 (t80) cc_final: 0.7147 (t80) REVERT: x 591 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7544 (ttt90) REVERT: j 57 TYR cc_start: 0.8879 (p90) cc_final: 0.8517 (p90) REVERT: k 62 TRP cc_start: 0.8602 (m100) cc_final: 0.8298 (m100) REVERT: k 98 MET cc_start: 0.8328 (tpp) cc_final: 0.8125 (tpp) REVERT: k 145 HIS cc_start: 0.7581 (m-70) cc_final: 0.7349 (m170) REVERT: k 167 GLU cc_start: 0.5577 (pm20) cc_final: 0.3677 (mp0) REVERT: l 33 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8856 (tm-30) REVERT: l 81 LEU cc_start: 0.8883 (tp) cc_final: 0.8565 (tt) REVERT: l 93 GLU cc_start: 0.8118 (pt0) cc_final: 0.7272 (pt0) REVERT: l 133 MET cc_start: 0.8250 (tmm) cc_final: 0.7820 (tmm) REVERT: l 282 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7913 (mm-30) REVERT: m 21 ILE cc_start: 0.9239 (mm) cc_final: 0.8861 (mt) REVERT: m 69 ILE cc_start: 0.8224 (tp) cc_final: 0.8000 (tt) REVERT: m 103 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8337 (mp) REVERT: m 209 MET cc_start: 0.8359 (pmm) cc_final: 0.8128 (pmm) REVERT: m 274 ILE cc_start: 0.8631 (mm) cc_final: 0.8277 (tp) REVERT: m 290 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8205 (tptt) REVERT: n 74 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8669 (tpt90) REVERT: n 92 ASP cc_start: 0.8131 (p0) cc_final: 0.7794 (p0) REVERT: n 93 TYR cc_start: 0.9048 (m-80) cc_final: 0.8355 (m-80) REVERT: n 132 ASP cc_start: 0.7556 (t0) cc_final: 0.6915 (t0) outliers start: 245 outliers final: 189 residues processed: 1168 average time/residue: 0.4651 time to fit residues: 934.1209 Evaluate side-chains 1160 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 951 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 310 SER Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 376 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 467 VAL Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 548 TYR Chi-restraints excluded: chain X residue 591 ARG Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 154 PHE Chi-restraints excluded: chain M residue 212 PHE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 78 MET Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 7 ILE Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 56 MET Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 123 HIS Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 209 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain e residue 231 MET Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 115 LEU Chi-restraints excluded: chain h residue 129 ASP Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain h residue 247 PHE Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 430 MET Chi-restraints excluded: chain h residue 458 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain h residue 480 VAL Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 72 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 310 SER Chi-restraints excluded: chain x residue 340 HIS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 467 VAL Chi-restraints excluded: chain x residue 514 ILE Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 548 TYR Chi-restraints excluded: chain x residue 554 ARG Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain x residue 606 LEU Chi-restraints excluded: chain x residue 610 LEU Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 114 ASP Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 234 VAL Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 255 LEU Chi-restraints excluded: chain l residue 292 GLN Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain m residue 49 LEU Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 212 PHE Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 259 LEU Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 44 ILE Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain n residue 129 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 3.9990 chunk 557 optimal weight: 0.8980 chunk 508 optimal weight: 8.9990 chunk 542 optimal weight: 0.9990 chunk 326 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 425 optimal weight: 0.1980 chunk 166 optimal weight: 6.9990 chunk 490 optimal weight: 0.5980 chunk 513 optimal weight: 7.9990 chunk 540 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 340 HIS ** L 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 359 ASN ** l 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 49624 Z= 0.206 Angle : 0.768 16.703 67458 Z= 0.375 Chirality : 0.044 0.330 7768 Planarity : 0.005 0.082 8248 Dihedral : 5.558 59.599 6656 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.36 % Favored : 89.59 % Rotamer: Outliers : 4.55 % Allowed : 28.53 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 1.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.11), residues: 6072 helix: -0.13 (0.09), residues: 3502 sheet: -2.97 (0.30), residues: 248 loop : -3.51 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 391 HIS 0.012 0.001 HIS l 326 PHE 0.043 0.002 PHE H 134 TYR 0.068 0.002 TYR L 26 ARG 0.007 0.000 ARG l 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1016 time to evaluate : 4.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7676 (t-100) cc_final: 0.7425 (t60) REVERT: A 83 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7075 (mm) REVERT: B 46 MET cc_start: 0.7494 (ttm) cc_final: 0.7283 (ttm) REVERT: B 67 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7175 (tp) REVERT: D 38 VAL cc_start: 0.8609 (t) cc_final: 0.8368 (p) REVERT: E 9 LEU cc_start: 0.8323 (tt) cc_final: 0.7451 (mt) REVERT: E 120 ILE cc_start: 0.8374 (mm) cc_final: 0.7985 (mt) REVERT: E 145 MET cc_start: 0.7808 (tpt) cc_final: 0.7532 (tpp) REVERT: E 193 TRP cc_start: 0.4207 (p-90) cc_final: 0.3631 (m-10) REVERT: E 229 ASP cc_start: 0.6621 (t0) cc_final: 0.6295 (m-30) REVERT: G 7 PHE cc_start: 0.7323 (t80) cc_final: 0.6893 (t80) REVERT: G 37 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7471 (tm-30) REVERT: H 27 LYS cc_start: 0.3978 (tptp) cc_final: 0.3727 (tptp) REVERT: H 37 ILE cc_start: 0.8655 (mm) cc_final: 0.8416 (tp) REVERT: H 79 PHE cc_start: 0.8131 (t80) cc_final: 0.7919 (t80) REVERT: H 96 LEU cc_start: 0.7723 (pp) cc_final: 0.7353 (tp) REVERT: H 112 MET cc_start: 0.7034 (ptp) cc_final: 0.6156 (ptp) REVERT: H 254 TYR cc_start: 0.8173 (t80) cc_final: 0.7646 (t80) REVERT: X 130 MET cc_start: 0.8475 (tmm) cc_final: 0.8159 (ppp) REVERT: X 310 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.9038 (p) REVERT: X 434 TYR cc_start: 0.7755 (t80) cc_final: 0.7057 (t80) REVERT: X 591 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7544 (ttt90) REVERT: J 57 TYR cc_start: 0.8930 (p90) cc_final: 0.8632 (p90) REVERT: K 50 ASN cc_start: 0.7825 (p0) cc_final: 0.7623 (p0) REVERT: K 98 MET cc_start: 0.8164 (tpp) cc_final: 0.7884 (tpp) REVERT: L 33 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8884 (tm-30) REVERT: L 93 GLU cc_start: 0.8158 (pt0) cc_final: 0.7441 (pt0) REVERT: L 133 MET cc_start: 0.8210 (tmm) cc_final: 0.7714 (tmm) REVERT: L 189 GLN cc_start: 0.7470 (tp40) cc_final: 0.7223 (tp40) REVERT: L 282 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7724 (mm-30) REVERT: L 326 HIS cc_start: 0.8241 (p90) cc_final: 0.8018 (p90) REVERT: M 21 ILE cc_start: 0.9249 (mm) cc_final: 0.8870 (mt) REVERT: M 35 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.8232 (mtp85) REVERT: M 103 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8479 (mp) REVERT: M 104 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6829 (mt-10) REVERT: M 290 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8192 (tptt) REVERT: N 43 PHE cc_start: 0.7128 (t80) cc_final: 0.6746 (t80) REVERT: N 74 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8705 (tpt90) REVERT: N 132 ASP cc_start: 0.7140 (t0) cc_final: 0.6761 (t0) REVERT: a 21 TRP cc_start: 0.7469 (t60) cc_final: 0.7131 (t60) REVERT: a 66 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6288 (m-80) REVERT: a 78 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7782 (mpp) REVERT: a 82 ASN cc_start: 0.8803 (t0) cc_final: 0.8578 (t0) REVERT: a 83 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6917 (mm) REVERT: a 91 HIS cc_start: 0.4223 (OUTLIER) cc_final: 0.3988 (t-170) REVERT: a 114 MET cc_start: 0.7498 (mtm) cc_final: 0.7217 (mtp) REVERT: c 21 LEU cc_start: 0.8261 (mm) cc_final: 0.7905 (tt) REVERT: c 34 ASN cc_start: 0.7655 (p0) cc_final: 0.7294 (p0) REVERT: c 36 MET cc_start: 0.8472 (ppp) cc_final: 0.8199 (ppp) REVERT: c 56 ILE cc_start: 0.6580 (pt) cc_final: 0.6348 (mm) REVERT: d 14 LEU cc_start: 0.8986 (tp) cc_final: 0.8758 (tp) REVERT: e 66 ASP cc_start: 0.7204 (m-30) cc_final: 0.6850 (t70) REVERT: e 120 ILE cc_start: 0.8669 (mm) cc_final: 0.8330 (mt) REVERT: e 168 MET cc_start: 0.5465 (mtt) cc_final: 0.5021 (mtp) REVERT: e 219 LYS cc_start: 0.9046 (tttp) cc_final: 0.8319 (tmmt) REVERT: g 7 PHE cc_start: 0.7343 (t80) cc_final: 0.7045 (t80) REVERT: g 24 LYS cc_start: 0.8136 (mttt) cc_final: 0.7492 (pttm) REVERT: g 37 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7534 (tm-30) REVERT: g 76 VAL cc_start: 0.9265 (p) cc_final: 0.9042 (p) REVERT: g 100 LYS cc_start: 0.8922 (mmtm) cc_final: 0.8669 (mmtt) REVERT: h 96 LEU cc_start: 0.7782 (pp) cc_final: 0.7215 (tp) REVERT: h 112 MET cc_start: 0.7012 (ptp) cc_final: 0.6274 (ptp) REVERT: h 134 PHE cc_start: 0.8476 (t80) cc_final: 0.8239 (t80) REVERT: h 158 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8330 (tm-30) REVERT: h 240 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8837 (tp) REVERT: h 254 TYR cc_start: 0.8003 (t80) cc_final: 0.7685 (t80) REVERT: h 279 MET cc_start: 0.7074 (mmp) cc_final: 0.6859 (ttp) REVERT: h 289 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8822 (tt) REVERT: h 379 ILE cc_start: 0.9106 (mm) cc_final: 0.8880 (mt) REVERT: h 407 TRP cc_start: 0.7843 (m100) cc_final: 0.7446 (m100) REVERT: x 13 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7548 (tt) REVERT: x 43 ILE cc_start: 0.7990 (mm) cc_final: 0.7525 (mt) REVERT: x 120 PHE cc_start: 0.7414 (t80) cc_final: 0.6837 (t80) REVERT: x 130 MET cc_start: 0.8503 (tmm) cc_final: 0.8142 (ppp) REVERT: x 300 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8571 (tp-100) REVERT: x 305 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8057 (ttpp) REVERT: x 310 SER cc_start: 0.9386 (OUTLIER) cc_final: 0.9071 (p) REVERT: x 373 MET cc_start: 0.7704 (ptp) cc_final: 0.7456 (ptp) REVERT: x 434 TYR cc_start: 0.7140 (t80) cc_final: 0.6898 (t80) REVERT: x 591 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7567 (ttt90) REVERT: j 57 TYR cc_start: 0.8851 (p90) cc_final: 0.8527 (p90) REVERT: k 62 TRP cc_start: 0.8551 (m100) cc_final: 0.8239 (m100) REVERT: l 33 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8869 (tm-30) REVERT: l 93 GLU cc_start: 0.8129 (pt0) cc_final: 0.7215 (pt0) REVERT: l 133 MET cc_start: 0.8344 (tmm) cc_final: 0.7822 (tmm) REVERT: l 282 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7880 (mm-30) REVERT: l 287 LEU cc_start: 0.8798 (mt) cc_final: 0.8510 (mt) REVERT: m 21 ILE cc_start: 0.9266 (mm) cc_final: 0.8906 (mt) REVERT: m 69 ILE cc_start: 0.8217 (tp) cc_final: 0.7989 (tt) REVERT: m 79 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7943 (pp) REVERT: m 103 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8321 (mp) REVERT: m 209 MET cc_start: 0.8330 (pmm) cc_final: 0.8120 (pmm) REVERT: m 226 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8076 (mmp) REVERT: m 274 ILE cc_start: 0.8565 (mm) cc_final: 0.8223 (tp) REVERT: m 290 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8218 (tptt) REVERT: n 66 MET cc_start: 0.8267 (tpt) cc_final: 0.8042 (tpp) REVERT: n 74 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8796 (tpt90) REVERT: n 92 ASP cc_start: 0.8099 (p0) cc_final: 0.7799 (p0) REVERT: n 93 TYR cc_start: 0.9037 (m-80) cc_final: 0.8311 (m-80) REVERT: n 132 ASP cc_start: 0.7424 (t0) cc_final: 0.6862 (t0) outliers start: 229 outliers final: 173 residues processed: 1169 average time/residue: 0.4502 time to fit residues: 901.2563 Evaluate side-chains 1161 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 968 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 310 SER Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 548 TYR Chi-restraints excluded: chain X residue 564 MET Chi-restraints excluded: chain X residue 591 ARG Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 212 PHE Chi-restraints excluded: chain M residue 226 MET Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 78 MET Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 91 HIS Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 73 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 7 ILE Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 123 HIS Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 115 LEU Chi-restraints excluded: chain h residue 129 ASP Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain h residue 247 PHE Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 311 LEU Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 430 MET Chi-restraints excluded: chain h residue 458 VAL Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 79 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 310 SER Chi-restraints excluded: chain x residue 340 HIS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 548 TYR Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 114 ASP Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 234 VAL Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 255 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 349 VAL Chi-restraints excluded: chain m residue 49 LEU Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 154 PHE Chi-restraints excluded: chain m residue 212 PHE Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 259 LEU Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 356 optimal weight: 3.9990 chunk 573 optimal weight: 4.9990 chunk 350 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 398 optimal weight: 6.9990 chunk 601 optimal weight: 2.9990 chunk 553 optimal weight: 7.9990 chunk 479 optimal weight: 5.9990 chunk 49 optimal weight: 0.0270 chunk 370 optimal weight: 10.0000 chunk 293 optimal weight: 0.7980 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 340 HIS ** L 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 GLN ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN ** l 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 113 GLN l 169 HIS l 326 HIS ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 164 GLN ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 49624 Z= 0.251 Angle : 0.787 16.878 67458 Z= 0.385 Chirality : 0.045 0.311 7768 Planarity : 0.005 0.080 8248 Dihedral : 5.564 59.816 6656 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.44 % Favored : 89.51 % Rotamer: Outliers : 4.19 % Allowed : 29.31 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 0.71 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.11), residues: 6072 helix: -0.12 (0.09), residues: 3498 sheet: -2.94 (0.30), residues: 248 loop : -3.49 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP H 391 HIS 0.012 0.001 HIS l 326 PHE 0.035 0.002 PHE H 134 TYR 0.054 0.002 TYR L 26 ARG 0.010 0.000 ARG L 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 981 time to evaluate : 4.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7718 (t-100) cc_final: 0.7459 (t60) REVERT: A 78 MET cc_start: 0.7954 (mtt) cc_final: 0.7566 (mpp) REVERT: A 83 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7130 (mm) REVERT: B 49 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: B 67 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7205 (tp) REVERT: D 38 VAL cc_start: 0.8634 (t) cc_final: 0.8402 (p) REVERT: D 70 PHE cc_start: 0.7638 (t80) cc_final: 0.7423 (t80) REVERT: E 8 VAL cc_start: 0.8775 (t) cc_final: 0.8475 (p) REVERT: E 120 ILE cc_start: 0.8392 (mm) cc_final: 0.7998 (mt) REVERT: E 145 MET cc_start: 0.7809 (tpt) cc_final: 0.7551 (tpp) REVERT: E 193 TRP cc_start: 0.4122 (p-90) cc_final: 0.3710 (m-10) REVERT: E 229 ASP cc_start: 0.6628 (t0) cc_final: 0.6342 (m-30) REVERT: G 7 PHE cc_start: 0.7363 (t80) cc_final: 0.6881 (t80) REVERT: H 27 LYS cc_start: 0.4091 (tptp) cc_final: 0.3834 (tptp) REVERT: H 37 ILE cc_start: 0.8658 (mm) cc_final: 0.8414 (tp) REVERT: H 79 PHE cc_start: 0.8168 (t80) cc_final: 0.7926 (t80) REVERT: H 96 LEU cc_start: 0.7826 (pp) cc_final: 0.7423 (tp) REVERT: H 112 MET cc_start: 0.6871 (ptp) cc_final: 0.6003 (ptp) REVERT: H 254 TYR cc_start: 0.8067 (t80) cc_final: 0.7509 (t80) REVERT: H 330 HIS cc_start: 0.8635 (t-90) cc_final: 0.8120 (t-170) REVERT: H 386 LEU cc_start: 0.6294 (tp) cc_final: 0.6070 (tt) REVERT: H 451 LEU cc_start: 0.7597 (mt) cc_final: 0.7387 (mt) REVERT: X 120 PHE cc_start: 0.7459 (t80) cc_final: 0.6761 (t80) REVERT: X 130 MET cc_start: 0.8502 (tmm) cc_final: 0.8266 (ppp) REVERT: X 310 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.9098 (p) REVERT: X 591 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7590 (ttt90) REVERT: J 57 TYR cc_start: 0.8988 (p90) cc_final: 0.8623 (p90) REVERT: K 50 ASN cc_start: 0.7942 (p0) cc_final: 0.7729 (p0) REVERT: K 98 MET cc_start: 0.8243 (tpp) cc_final: 0.8031 (tpp) REVERT: L 33 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8921 (tm-30) REVERT: L 93 GLU cc_start: 0.8128 (pt0) cc_final: 0.7464 (pt0) REVERT: L 133 MET cc_start: 0.8240 (tmm) cc_final: 0.7759 (tmm) REVERT: L 189 GLN cc_start: 0.7534 (tp40) cc_final: 0.7314 (tp40) REVERT: M 21 ILE cc_start: 0.9256 (mm) cc_final: 0.8877 (mt) REVERT: M 35 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.8214 (mtp85) REVERT: M 103 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8487 (mp) REVERT: M 104 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6961 (mt-10) REVERT: M 112 PHE cc_start: 0.8174 (t80) cc_final: 0.7939 (t80) REVERT: M 290 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8142 (tptt) REVERT: N 74 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8747 (tpt90) REVERT: N 132 ASP cc_start: 0.7352 (t0) cc_final: 0.6905 (t70) REVERT: a 21 TRP cc_start: 0.7552 (t60) cc_final: 0.7162 (t60) REVERT: a 66 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: a 78 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7812 (mpp) REVERT: a 83 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6923 (mm) REVERT: a 114 MET cc_start: 0.7507 (mtm) cc_final: 0.7186 (mtp) REVERT: c 21 LEU cc_start: 0.8276 (mm) cc_final: 0.7942 (tt) REVERT: c 36 MET cc_start: 0.8491 (ppp) cc_final: 0.8265 (ppp) REVERT: c 56 ILE cc_start: 0.6555 (pt) cc_final: 0.6337 (mm) REVERT: d 14 LEU cc_start: 0.9027 (tp) cc_final: 0.8808 (tp) REVERT: d 78 TYR cc_start: 0.6820 (m-10) cc_final: 0.6537 (m-10) REVERT: e 66 ASP cc_start: 0.7156 (m-30) cc_final: 0.6911 (t70) REVERT: e 119 TYR cc_start: 0.8633 (t80) cc_final: 0.8312 (t80) REVERT: e 120 ILE cc_start: 0.8615 (mm) cc_final: 0.8265 (mt) REVERT: e 168 MET cc_start: 0.5734 (mtt) cc_final: 0.5195 (mtp) REVERT: e 219 LYS cc_start: 0.9054 (tttp) cc_final: 0.8721 (tmmt) REVERT: g 24 LYS cc_start: 0.8127 (mttt) cc_final: 0.7486 (pttm) REVERT: g 37 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7545 (tm-30) REVERT: g 76 VAL cc_start: 0.9286 (p) cc_final: 0.9035 (p) REVERT: g 100 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8717 (mmtt) REVERT: h 96 LEU cc_start: 0.7861 (pp) cc_final: 0.7264 (tp) REVERT: h 112 MET cc_start: 0.7034 (ptp) cc_final: 0.6147 (ptp) REVERT: h 158 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8377 (tm-30) REVERT: h 240 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8831 (tp) REVERT: h 254 TYR cc_start: 0.7995 (t80) cc_final: 0.7466 (t80) REVERT: h 279 MET cc_start: 0.7107 (mmp) cc_final: 0.6864 (ttp) REVERT: h 289 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8847 (tt) REVERT: h 379 ILE cc_start: 0.9113 (mm) cc_final: 0.8908 (mt) REVERT: h 407 TRP cc_start: 0.7774 (m100) cc_final: 0.7272 (m100) REVERT: x 13 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7608 (tt) REVERT: x 120 PHE cc_start: 0.7473 (t80) cc_final: 0.7072 (t80) REVERT: x 130 MET cc_start: 0.8501 (tmm) cc_final: 0.8233 (ppp) REVERT: x 300 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8769 (tp-100) REVERT: x 303 ILE cc_start: 0.9080 (tp) cc_final: 0.8876 (tp) REVERT: x 305 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8425 (ttpp) REVERT: x 310 SER cc_start: 0.9428 (OUTLIER) cc_final: 0.9115 (p) REVERT: x 379 MET cc_start: 0.7849 (mmt) cc_final: 0.7333 (mmt) REVERT: x 417 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8290 (tmm) REVERT: x 434 TYR cc_start: 0.7261 (t80) cc_final: 0.6964 (t80) REVERT: x 591 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7578 (ttt90) REVERT: j 57 TYR cc_start: 0.8926 (p90) cc_final: 0.8587 (p90) REVERT: k 62 TRP cc_start: 0.8558 (m100) cc_final: 0.8288 (m100) REVERT: k 106 PRO cc_start: 0.9103 (Cg_endo) cc_final: 0.8854 (Cg_exo) REVERT: l 26 TYR cc_start: 0.8954 (p90) cc_final: 0.8700 (p90) REVERT: l 33 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8909 (tm-30) REVERT: l 93 GLU cc_start: 0.8185 (pt0) cc_final: 0.7379 (pt0) REVERT: l 133 MET cc_start: 0.8352 (tmm) cc_final: 0.7863 (tmm) REVERT: l 282 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7921 (mm-30) REVERT: m 20 PHE cc_start: 0.8234 (m-10) cc_final: 0.7972 (m-80) REVERT: m 21 ILE cc_start: 0.9259 (mm) cc_final: 0.8880 (mt) REVERT: m 69 ILE cc_start: 0.8267 (tp) cc_final: 0.8033 (tt) REVERT: m 103 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8326 (mp) REVERT: m 166 MET cc_start: 0.8081 (ppp) cc_final: 0.7252 (ppp) REVERT: m 209 MET cc_start: 0.8415 (pmm) cc_final: 0.8164 (pmm) REVERT: m 274 ILE cc_start: 0.8606 (mm) cc_final: 0.8270 (tp) REVERT: m 290 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8181 (tptt) REVERT: n 74 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8846 (tpt90) REVERT: n 92 ASP cc_start: 0.8167 (p0) cc_final: 0.7841 (p0) REVERT: n 93 TYR cc_start: 0.9083 (m-80) cc_final: 0.8544 (m-80) REVERT: n 132 ASP cc_start: 0.7667 (t0) cc_final: 0.6987 (t0) outliers start: 211 outliers final: 180 residues processed: 1129 average time/residue: 0.4541 time to fit residues: 887.3472 Evaluate side-chains 1156 residues out of total 5044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 957 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 213 TYR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 334 HIS Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 430 MET Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 141 TYR Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain X residue 258 TYR Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 310 SER Chi-restraints excluded: chain X residue 351 VAL Chi-restraints excluded: chain X residue 376 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 448 VAL Chi-restraints excluded: chain X residue 529 VAL Chi-restraints excluded: chain X residue 532 VAL Chi-restraints excluded: chain X residue 544 VAL Chi-restraints excluded: chain X residue 548 TYR Chi-restraints excluded: chain X residue 591 ARG Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 41 TYR Chi-restraints excluded: chain J residue 56 GLN Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 171 TRP Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 71 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 318 VAL Chi-restraints excluded: chain L residue 349 VAL Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain M residue 212 PHE Chi-restraints excluded: chain M residue 226 MET Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 39 PHE Chi-restraints excluded: chain a residue 66 TYR Chi-restraints excluded: chain a residue 78 MET Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain a residue 110 ASN Chi-restraints excluded: chain a residue 156 THR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 113 LEU Chi-restraints excluded: chain c residue 115 ARG Chi-restraints excluded: chain d residue 7 ILE Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 72 PHE Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain e residue 16 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 101 VAL Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain e residue 180 ILE Chi-restraints excluded: chain e residue 213 TYR Chi-restraints excluded: chain e residue 227 ILE Chi-restraints excluded: chain g residue 40 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 115 LEU Chi-restraints excluded: chain h residue 129 ASP Chi-restraints excluded: chain h residue 207 VAL Chi-restraints excluded: chain h residue 221 GLU Chi-restraints excluded: chain h residue 225 LEU Chi-restraints excluded: chain h residue 240 ILE Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 334 HIS Chi-restraints excluded: chain h residue 430 MET Chi-restraints excluded: chain h residue 477 ILE Chi-restraints excluded: chain h residue 480 VAL Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 13 ILE Chi-restraints excluded: chain x residue 205 LEU Chi-restraints excluded: chain x residue 258 TYR Chi-restraints excluded: chain x residue 299 LEU Chi-restraints excluded: chain x residue 305 LYS Chi-restraints excluded: chain x residue 310 SER Chi-restraints excluded: chain x residue 340 HIS Chi-restraints excluded: chain x residue 351 VAL Chi-restraints excluded: chain x residue 401 LEU Chi-restraints excluded: chain x residue 417 MET Chi-restraints excluded: chain x residue 448 VAL Chi-restraints excluded: chain x residue 529 VAL Chi-restraints excluded: chain x residue 532 VAL Chi-restraints excluded: chain x residue 544 VAL Chi-restraints excluded: chain x residue 548 TYR Chi-restraints excluded: chain x residue 591 ARG Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 41 TYR Chi-restraints excluded: chain j residue 56 GLN Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 120 ILE Chi-restraints excluded: chain j residue 154 GLU Chi-restraints excluded: chain j residue 171 TRP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 114 ASP Chi-restraints excluded: chain k residue 117 ASP Chi-restraints excluded: chain l residue 126 THR Chi-restraints excluded: chain l residue 167 VAL Chi-restraints excluded: chain l residue 197 LEU Chi-restraints excluded: chain l residue 199 ASP Chi-restraints excluded: chain l residue 234 VAL Chi-restraints excluded: chain l residue 235 THR Chi-restraints excluded: chain l residue 244 VAL Chi-restraints excluded: chain l residue 255 LEU Chi-restraints excluded: chain l residue 318 VAL Chi-restraints excluded: chain l residue 326 HIS Chi-restraints excluded: chain l residue 349 VAL Chi-restraints excluded: chain m residue 49 LEU Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 154 PHE Chi-restraints excluded: chain m residue 212 PHE Chi-restraints excluded: chain m residue 226 MET Chi-restraints excluded: chain m residue 259 LEU Chi-restraints excluded: chain m residue 283 PHE Chi-restraints excluded: chain m residue 306 MET Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 380 optimal weight: 2.9990 chunk 510 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 441 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 479 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 492 optimal weight: 0.2980 chunk 60 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 ASN ** X 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 340 HIS ** L 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 ASN ** l 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 164 GLN ** m 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.116798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102476 restraints weight = 98503.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106115 restraints weight = 125283.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105401 restraints weight = 58994.496| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 49624 Z= 0.257 Angle : 0.792 17.023 67458 Z= 0.387 Chirality : 0.045 0.310 7768 Planarity : 0.005 0.071 8248 Dihedral : 5.566 59.904 6655 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.61 % Favored : 89.34 % Rotamer: Outliers : 4.17 % Allowed : 29.75 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.10 % Twisted Proline : 0.71 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.11), residues: 6072 helix: -0.09 (0.09), residues: 3486 sheet: -2.88 (0.30), residues: 252 loop : -3.46 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 391 HIS 0.020 0.001 HIS l 326 PHE 0.031 0.002 PHE m 112 TYR 0.050 0.002 TYR L 26 ARG 0.009 0.000 ARG j 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13566.72 seconds wall clock time: 233 minutes 54.75 seconds (14034.75 seconds total)