Starting phenix.real_space_refine on Mon Sep 30 04:46:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syh_25528/09_2024/7syh_25528.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syh_25528/09_2024/7syh_25528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syh_25528/09_2024/7syh_25528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syh_25528/09_2024/7syh_25528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syh_25528/09_2024/7syh_25528.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syh_25528/09_2024/7syh_25528.cif" } resolution = 4.6 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1858 5.49 5 S 180 5.16 5 C 42397 2.51 5 N 14495 2.21 5 O 19829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 78761 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 142, 'rna2p_pyr': 111, 'rna3p_pur': 755, 'rna3p_pyr': 689} Link IDs: {'rna2p': 252, 'rna3p': 1444} Chain breaks: 11 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1233 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 956 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "z" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3465 Classifications: {'RNA': 162} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 14, 'rna3p_pur': 74, 'rna3p_pyr': 64} Link IDs: {'rna2p': 23, 'rna3p': 138} Chain breaks: 1 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69331 SG CYS b 23 90.226 130.351 134.545 1.00 68.16 S ATOM 69352 SG CYS b 26 93.578 130.385 135.421 1.00 66.89 S ATOM 69735 SG CYS b 74 92.709 127.448 136.042 1.00 58.95 S ATOM 69754 SG CYS b 77 92.795 129.587 137.918 1.00 60.11 S ATOM 72396 SG CYS g 121 147.752 100.339 241.245 1.00257.96 S ATOM 72432 SG CYS g 126 145.758 98.165 238.434 1.00261.29 S ATOM 72550 SG CYS g 141 147.388 101.453 238.444 1.00271.87 S ATOM 72569 SG CYS g 144 144.007 100.584 239.614 1.00263.31 S Time building chain proxies: 32.39, per 1000 atoms: 0.41 Number of scatterers: 78761 At special positions: 0 Unit cell: (231.8, 194.75, 258.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 180 16.00 P 1858 15.00 O 19829 8.00 N 14495 7.00 C 42397 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: 13.89 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " Number of angles added : 12 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9066 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 57 sheets defined 33.1% alpha, 14.6% beta 467 base pairs and 935 stacking pairs defined. Time for finding SS restraints: 24.96 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.560A pdb=" N TYR B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.845A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.595A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 178 removed outlier: 3.835A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 191 through 200 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.866A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.936A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 6.208A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 54 through 60 removed outlier: 3.936A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 60' Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.566A pdb=" N ARG E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 109 removed outlier: 3.797A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 removed outlier: 3.845A pdb=" N ALA E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 167 removed outlier: 3.873A pdb=" N TYR E 166 " --> pdb=" O PRO E 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.601A pdb=" N VAL F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 61 through 66 removed outlier: 3.552A pdb=" N ALA G 64 " --> pdb=" O PHE G 61 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN G 65 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 75 removed outlier: 4.000A pdb=" N THR G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 4.113A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR G 104 " --> pdb=" O ILE G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.752A pdb=" N ILE G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.814A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 203 removed outlier: 3.984A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.514A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 removed outlier: 3.750A pdb=" N SER I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 removed outlier: 3.843A pdb=" N ALA I 38 " --> pdb=" O ASP I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 87 removed outlier: 3.584A pdb=" N PHE I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS I 74 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN I 76 " --> pdb=" O PHE I 72 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL I 77 " --> pdb=" O GLN I 73 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU I 79 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.925A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 134 through 139 Processing helix chain 'J' and resid 142 through 155 removed outlier: 3.699A pdb=" N ASN J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 removed outlier: 3.796A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 34 removed outlier: 3.531A pdb=" N LEU K 25 " --> pdb=" O GLU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.524A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 removed outlier: 3.524A pdb=" N GLY K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 97 removed outlier: 3.834A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 107 removed outlier: 3.799A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.623A pdb=" N GLY K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 163 through 167 removed outlier: 3.825A pdb=" N GLY K 167 " --> pdb=" O PRO K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 186 removed outlier: 3.699A pdb=" N ARG K 175 " --> pdb=" O GLY K 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.529A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 35 through 44 Processing helix chain 'N' and resid 60 through 70 removed outlier: 3.995A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 90 removed outlier: 3.688A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL N 89 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 43 Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 62 through 67 removed outlier: 4.073A pdb=" N VAL O 66 " --> pdb=" O GLN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 105 removed outlier: 3.890A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'O' and resid 142 through 147 removed outlier: 4.301A pdb=" N SER O 147 " --> pdb=" O SER O 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 62 removed outlier: 4.522A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 62' Processing helix chain 'P' and resid 70 through 89 removed outlier: 3.757A pdb=" N GLY P 89 " --> pdb=" O CYS P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 121 removed outlier: 4.521A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.878A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 47 removed outlier: 3.945A pdb=" N ARG Q 47 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'R' and resid 47 through 59 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 77 through 99 removed outlier: 3.814A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 4.097A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.629A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 39 Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 99 through 110 removed outlier: 3.751A pdb=" N LEU S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP S 110 " --> pdb=" O LEU S 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 33 removed outlier: 3.765A pdb=" N ALA T 29 " --> pdb=" O ILE T 26 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE T 30 " --> pdb=" O ALA T 27 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR T 31 " --> pdb=" O PHE T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 48 removed outlier: 4.101A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL T 44 " --> pdb=" O TYR T 40 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG T 46 " --> pdb=" O HIS T 42 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS T 47 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.609A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 13 through 26 Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 71 through 79 removed outlier: 3.691A pdb=" N ILE U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 110 Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 29 through 46 Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.707A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 4.475A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'X' and resid 5 through 20 Processing helix chain 'X' and resid 31 through 45 Processing helix chain 'X' and resid 85 through 91 removed outlier: 3.655A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 120 removed outlier: 3.813A pdb=" N ARG X 118 " --> pdb=" O GLU X 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 23 Processing helix chain 'Y' and resid 24 through 31 Processing helix chain 'Y' and resid 32 through 39 removed outlier: 3.879A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 3.766A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 87 through 95 removed outlier: 3.771A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 116 removed outlier: 3.798A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 126 Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.520A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 78 Processing helix chain 'a' and resid 80 through 95 Processing helix chain 'b' and resid 49 through 56 removed outlier: 3.522A pdb=" N ALA b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'b' and resid 89 through 94 removed outlier: 3.509A pdb=" N ARG b 92 " --> pdb=" O ARG b 89 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS b 93 " --> pdb=" O GLU b 90 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP b 94 " --> pdb=" O ALA b 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 89 through 94' Processing helix chain 'c' and resid 11 through 18 removed outlier: 4.181A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 14 through 19 removed outlier: 3.699A pdb=" N SER e 18 " --> pdb=" O PHE e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.615A pdb=" N GLY e 35 " --> pdb=" O ARG e 32 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU e 36 " --> pdb=" O LYS e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 36' Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'g' and resid 101 through 105 Processing helix chain 'n' and resid 2 through 25 removed outlier: 3.673A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.159A pdb=" N ILE B 48 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.535A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 147 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 32 Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.535A pdb=" N LEU C 86 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET C 103 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ARG C 213 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 138 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL C 215 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG C 136 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET C 217 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU C 134 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 104 through 106 removed outlier: 3.550A pdb=" N VAL D 112 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AA7, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AA8, first strand: chain 'E' and resid 36 through 42 removed outlier: 3.522A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 38 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE E 49 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU E 47 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR E 42 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 45 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 137 through 138 Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 176 removed outlier: 3.608A pdb=" N ARG E 173 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.697A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.741A pdb=" N GLU F 97 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.657A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 110 " --> pdb=" O ILE F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.537A pdb=" N ILE F 147 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N HIS F 138 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE F 129 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL F 140 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 217 through 221 removed outlier: 7.278A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY F 193 " --> pdb=" O CYS F 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU F 180 " --> pdb=" O GLY F 229 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY F 229 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET F 182 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL F 227 " --> pdb=" O MET F 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 123 through 124 removed outlier: 3.590A pdb=" N ASP G 124 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.713A pdb=" N VAL H 108 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY H 55 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN H 110 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 53 " --> pdb=" O ASN H 110 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 50 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL H 36 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.831A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 160 through 162 removed outlier: 4.516A pdb=" N LYS H 160 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 47 through 51 removed outlier: 4.069A pdb=" N ALA I 47 " --> pdb=" O PHE I 63 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL I 93 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE I 95 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 141 through 146 removed outlier: 3.862A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ARG I 152 " --> pdb=" O ASP I 184 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 42 through 47 removed outlier: 6.906A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.826A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ARG J 77 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP J 105 " --> pdb=" O ARG J 77 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE J 175 " --> pdb=" O CYS J 100 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA J 173 " --> pdb=" O VAL J 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AC7, first strand: chain 'L' and resid 61 through 63 Processing sheet with id=AC8, first strand: chain 'M' and resid 72 through 79 removed outlier: 7.145A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY M 75 " --> pdb=" O VAL M 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 91 through 94 Processing sheet with id=AD1, first strand: chain 'N' and resid 77 through 79 removed outlier: 4.041A pdb=" N ILE N 77 " --> pdb=" O CYS N 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.122A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE P 95 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE P 129 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU P 97 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASP P 131 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 75 through 77 removed outlier: 3.793A pdb=" N THR Q 101 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 20 through 24 removed outlier: 3.956A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS R 33 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL R 72 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 96 through 98 removed outlier: 5.869A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'U' and resid 81 through 82 removed outlier: 4.056A pdb=" N GLY U 81 " --> pdb=" O SER U 93 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER U 93 " --> pdb=" O GLY U 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AD8, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.562A pdb=" N LEU V 88 " --> pdb=" O VAL V 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE V 89 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE V 22 " --> pdb=" O ILE V 89 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 59 through 66 removed outlier: 3.547A pdb=" N ILE V 84 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 35 through 37 removed outlier: 3.608A pdb=" N VAL W 36 " --> pdb=" O LYS W 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 24 through 27 removed outlier: 3.585A pdb=" N VAL X 25 " --> pdb=" O VAL X 63 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 71 through 74 removed outlier: 4.034A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE X 128 " --> pdb=" O GLY X 73 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY X 127 " --> pdb=" O VAL X 103 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL X 103 " --> pdb=" O GLY X 127 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 80 through 84 removed outlier: 7.602A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU Y 52 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS Y 124 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 6 through 15 removed outlier: 3.577A pdb=" N THR Z 6 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY Z 71 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL Z 27 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LYS Z 68 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR Z 62 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 97 through 101 removed outlier: 4.108A pdb=" N VAL a 100 " --> pdb=" O ILE a 108 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AE8, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.815A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'c' and resid 43 through 47 removed outlier: 3.666A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER c 78 " --> pdb=" O LYS c 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 54 through 55 removed outlier: 7.346A pdb=" N VAL c 54 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU c 63 " --> pdb=" O VAL c 54 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 27 through 33 removed outlier: 7.840A pdb=" N CYS d 27 " --> pdb=" O GLY d 19 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLY d 19 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 30 through 31 Processing sheet with id=AF4, first strand: chain 'g' and resid 133 through 134 Processing sheet with id=AF5, first strand: chain 'h' and resid 9 through 11 removed outlier: 3.790A pdb=" N GLY h 9 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL h 309 " --> pdb=" O GLY h 9 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 18 through 22 removed outlier: 3.641A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP h 43 " --> pdb=" O ILE h 31 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER h 33 " --> pdb=" O ILE h 41 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 18 through 22 removed outlier: 3.641A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP h 43 " --> pdb=" O ILE h 31 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER h 33 " --> pdb=" O ILE h 41 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.770A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 108 through 113 removed outlier: 3.816A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU h 131 " --> pdb=" O LYS h 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 151 through 156 removed outlier: 6.264A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 195 through 200 removed outlier: 6.573A pdb=" N GLY h 210 " --> pdb=" O ASN h 196 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL h 198 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA h 208 " --> pdb=" O VAL h 198 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL h 200 " --> pdb=" O LEU h 206 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU h 206 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS h 207 " --> pdb=" O TRP h 219 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.543A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP h 259 " --> pdb=" O LEU h 248 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) 1326 hydrogen bonds defined for protein. 3807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1183 hydrogen bonds 1988 hydrogen bond angles 0 basepair planarities 467 basepair parallelities 935 stacking parallelities Total time for adding SS restraints: 61.41 Time building geometry restraints manager: 17.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11510 1.33 - 1.45: 32620 1.45 - 1.58: 35996 1.58 - 1.70: 3705 1.70 - 1.83: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" C VAL a 62 " pdb=" N PRO a 63 " ideal model delta sigma weight residual 1.334 1.377 -0.044 8.40e-03 1.42e+04 2.69e+01 bond pdb=" CA GLU N 117 " pdb=" CB GLU N 117 " ideal model delta sigma weight residual 1.526 1.601 -0.075 1.53e-02 4.27e+03 2.40e+01 bond pdb=" C ILE C 189 " pdb=" N PRO C 190 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.04e+00 bond pdb=" C GLN Y 61 " pdb=" N PRO Y 62 " ideal model delta sigma weight residual 1.334 1.388 -0.055 2.34e-02 1.83e+03 5.44e+00 bond pdb=" CA ARG D 166 " pdb=" CB ARG D 166 " ideal model delta sigma weight residual 1.527 1.556 -0.030 1.27e-02 6.20e+03 5.42e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 121133 3.10 - 6.21: 1108 6.21 - 9.31: 179 9.31 - 12.42: 25 12.42 - 15.52: 4 Bond angle restraints: 122449 Sorted by residual: angle pdb=" N GLN H 197 " pdb=" CA GLN H 197 " pdb=" CB GLN H 197 " ideal model delta sigma weight residual 110.40 119.91 -9.51 1.63e+00 3.76e-01 3.40e+01 angle pdb=" C3' G 2 752 " pdb=" O3' G 2 752 " pdb=" P C 2 753 " ideal model delta sigma weight residual 120.20 127.62 -7.42 1.50e+00 4.44e-01 2.45e+01 angle pdb=" C3' U 2 553 " pdb=" O3' U 2 553 " pdb=" P A 2 554 " ideal model delta sigma weight residual 120.20 127.49 -7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " pdb=" P U 2 689 " ideal model delta sigma weight residual 120.20 127.44 -7.24 1.50e+00 4.44e-01 2.33e+01 angle pdb=" CA PRO D 210 " pdb=" N PRO D 210 " pdb=" CD PRO D 210 " ideal model delta sigma weight residual 112.00 105.39 6.61 1.40e+00 5.10e-01 2.23e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 48607 35.88 - 71.76: 4492 71.76 - 107.64: 582 107.64 - 143.52: 9 143.52 - 179.40: 24 Dihedral angle restraints: 53714 sinusoidal: 39658 harmonic: 14056 Sorted by residual: dihedral pdb=" O4' U 21624 " pdb=" C1' U 21624 " pdb=" N1 U 21624 " pdb=" C2 U 21624 " ideal model delta sinusoidal sigma weight residual -160.00 17.40 -177.40 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 34.71 165.29 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual -160.00 2.36 -162.36 1 1.50e+01 4.44e-03 8.33e+01 ... (remaining 53711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 13820 0.067 - 0.134: 1225 0.134 - 0.201: 125 0.201 - 0.269: 17 0.269 - 0.336: 7 Chirality restraints: 15194 Sorted by residual: chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA VAL D 209 " pdb=" N VAL D 209 " pdb=" C VAL D 209 " pdb=" CB VAL D 209 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C3' U z 160 " pdb=" C4' U z 160 " pdb=" O3' U z 160 " pdb=" C2' U z 160 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 209 " -0.081 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO D 210 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO D 210 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO D 210 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 129 " 0.322 9.50e-02 1.11e+02 1.45e-01 1.34e+01 pdb=" NE ARG U 129 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG U 129 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG U 129 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG U 129 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 120 " -0.019 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR E 120 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR E 120 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 120 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR E 120 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 120 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 120 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 120 " -0.001 2.00e-02 2.50e+03 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 15345 2.78 - 3.31: 64684 3.31 - 3.84: 149823 3.84 - 4.37: 168719 4.37 - 4.90: 249989 Nonbonded interactions: 648560 Sorted by model distance: nonbonded pdb=" O2' G 21121 " pdb=" O ILE C 204 " model vdw 2.250 3.040 nonbonded pdb=" O TYR D 266 " pdb=" OG1 THR D 270 " model vdw 2.276 3.040 nonbonded pdb=" O2' G 21528 " pdb=" OP1 C 21666 " model vdw 2.277 3.040 nonbonded pdb=" O VAL U 72 " pdb=" OG1 THR U 76 " model vdw 2.278 3.040 nonbonded pdb=" O2' G 21611 " pdb=" O GLN T 87 " model vdw 2.284 3.040 ... (remaining 648555 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.770 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: 0.070 Extract box with map and model: 2.640 Check model and map are aligned: 0.470 Set scattering table: 0.560 Process input model: 188.120 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 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 : 0.003 0.075 84105 Z= 0.197 Angle : 0.785 15.521 122449 Z= 0.380 Chirality : 0.039 0.336 15194 Planarity : 0.006 0.145 8634 Dihedral : 21.813 179.398 44648 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.75 % Favored : 94.23 % Rotamer: Outliers : 0.02 % Allowed : 0.66 % Favored : 99.31 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.97 (0.10), residues: 4821 helix: -1.82 (0.11), residues: 1465 sheet: -1.34 (0.19), residues: 706 loop : -2.28 (0.11), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 256 HIS 0.020 0.001 HIS N 28 PHE 0.043 0.002 PHE B 32 TYR 0.061 0.002 TYR L 12 ARG 0.013 0.000 ARG U 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 964 time to evaluate : 4.414 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: symmetry clash REVERT: B 58 LEU cc_start: 0.7685 (mm) cc_final: 0.7142 (mm) REVERT: B 75 SER cc_start: 0.8505 (p) cc_final: 0.8249 (p) REVERT: B 120 ARG cc_start: 0.5590 (mmm-85) cc_final: 0.5183 (mmm160) REVERT: B 195 TRP cc_start: 0.6266 (p-90) cc_final: 0.5541 (p-90) REVERT: C 87 ILE cc_start: 0.7358 (tt) cc_final: 0.6566 (pt) REVERT: C 147 ASN cc_start: 0.8632 (m-40) cc_final: 0.8430 (p0) REVERT: D 60 TRP cc_start: 0.2588 (t60) cc_final: 0.2091 (t60) REVERT: D 65 LYS cc_start: 0.6827 (pttm) cc_final: 0.6496 (ptpt) REVERT: D 83 LEU cc_start: 0.7725 (mp) cc_final: 0.7200 (mp) REVERT: D 110 MET cc_start: 0.7192 (tpt) cc_final: 0.6931 (tpp) REVERT: D 124 PHE cc_start: 0.6619 (m-10) cc_final: 0.6181 (m-80) REVERT: D 143 CYS cc_start: 0.7171 (t) cc_final: 0.6475 (p) REVERT: D 166 ARG cc_start: 0.5489 (ptm-80) cc_final: 0.5264 (ttt-90) REVERT: D 176 LYS cc_start: 0.6879 (mttm) cc_final: 0.6146 (tptm) REVERT: D 212 LYS cc_start: 0.7337 (ptpp) cc_final: 0.6893 (ptmm) REVERT: D 254 ASP cc_start: 0.7539 (m-30) cc_final: 0.7114 (p0) REVERT: D 266 TYR cc_start: 0.5222 (m-10) cc_final: 0.4644 (m-80) REVERT: E 1 MET cc_start: 0.1167 (ptt) cc_final: 0.0152 (tpt) REVERT: E 157 MET cc_start: 0.5825 (tpt) cc_final: 0.4855 (tpt) REVERT: F 19 MET cc_start: 0.6869 (mmm) cc_final: 0.6418 (tpp) REVERT: F 87 MET cc_start: 0.5489 (tpt) cc_final: 0.4893 (tpt) REVERT: F 125 LYS cc_start: 0.7291 (tttt) cc_final: 0.6926 (tttm) REVERT: F 127 ARG cc_start: 0.6943 (mmt90) cc_final: 0.6629 (ttm110) REVERT: F 228 ILE cc_start: 0.7791 (pt) cc_final: 0.7531 (pt) REVERT: G 38 TYR cc_start: 0.4615 (m-80) cc_final: 0.4129 (m-10) REVERT: G 42 LYS cc_start: 0.4717 (mppt) cc_final: 0.4267 (tptm) REVERT: G 48 TYR cc_start: 0.3914 (m-80) cc_final: 0.3677 (m-80) REVERT: G 77 MET cc_start: 0.2695 (mpp) cc_final: 0.2452 (mpp) REVERT: G 78 MET cc_start: 0.2675 (pmm) cc_final: 0.2245 (ptp) REVERT: G 82 ASN cc_start: 0.4075 (m-40) cc_final: 0.3411 (t0) REVERT: G 124 ASP cc_start: 0.4801 (p0) cc_final: 0.4252 (p0) REVERT: G 128 ILE cc_start: 0.2045 (mm) cc_final: 0.1490 (mt) REVERT: H 31 ARG cc_start: 0.6684 (ptp-110) cc_final: 0.5828 (mtt180) REVERT: H 52 ILE cc_start: 0.6200 (pt) cc_final: 0.5622 (pt) REVERT: H 105 ASN cc_start: 0.7361 (t0) cc_final: 0.7159 (t0) REVERT: H 115 LYS cc_start: 0.7302 (tmmt) cc_final: 0.7027 (tppt) REVERT: I 32 MET cc_start: 0.5488 (tpp) cc_final: 0.5209 (tpp) REVERT: I 94 PHE cc_start: 0.5010 (m-10) cc_final: 0.4480 (m-80) REVERT: I 131 GLU cc_start: 0.7111 (pp20) cc_final: 0.6648 (tm-30) REVERT: J 27 TYR cc_start: 0.7026 (p90) cc_final: 0.6423 (p90) REVERT: J 205 ARG cc_start: 0.6448 (tpt90) cc_final: 0.6176 (ttm-80) REVERT: K 27 GLN cc_start: 0.7374 (tp-100) cc_final: 0.6652 (tm-30) REVERT: K 45 ARG cc_start: 0.5667 (ttp-170) cc_final: 0.4971 (mtp180) REVERT: K 59 GLU cc_start: 0.6883 (tp30) cc_final: 0.6563 (tp30) REVERT: K 65 GLU cc_start: 0.5047 (tp30) cc_final: 0.3856 (pm20) REVERT: K 66 LYS cc_start: 0.6205 (mmtt) cc_final: 0.4517 (ttmm) REVERT: K 67 ASP cc_start: 0.6677 (t70) cc_final: 0.6343 (t0) REVERT: K 108 ARG cc_start: 0.7793 (mmm160) cc_final: 0.6812 (tpp80) REVERT: K 148 ILE cc_start: 0.8439 (mm) cc_final: 0.8157 (mm) REVERT: K 152 ASP cc_start: 0.7279 (p0) cc_final: 0.6835 (m-30) REVERT: L 17 LYS cc_start: 0.7493 (mtmm) cc_final: 0.6918 (tptp) REVERT: L 21 MET cc_start: 0.3186 (ptm) cc_final: 0.2715 (ptt) REVERT: L 25 LYS cc_start: 0.5550 (tttt) cc_final: 0.5178 (ttpp) REVERT: L 45 VAL cc_start: 0.6554 (t) cc_final: 0.6216 (t) REVERT: L 57 TYR cc_start: 0.4783 (m-10) cc_final: 0.4345 (m-80) REVERT: L 64 TRP cc_start: 0.3654 (m-10) cc_final: 0.3238 (m-10) REVERT: L 74 GLU cc_start: 0.3872 (pp20) cc_final: 0.3172 (tt0) REVERT: M 95 TYR cc_start: 0.7279 (t80) cc_final: 0.6614 (t80) REVERT: M 104 LYS cc_start: 0.5879 (ptmm) cc_final: 0.5590 (ptmt) REVERT: M 109 MET cc_start: 0.6644 (ptp) cc_final: 0.6131 (ptm) REVERT: M 118 ARG cc_start: 0.5576 (mtm-85) cc_final: 0.4556 (ttm110) REVERT: M 124 ASP cc_start: 0.7241 (m-30) cc_final: 0.6581 (m-30) REVERT: N 49 LEU cc_start: 0.1231 (pt) cc_final: 0.1007 (mp) REVERT: N 121 LYS cc_start: -0.2000 (tptt) cc_final: -0.2340 (mmmt) REVERT: O 16 LEU cc_start: 0.8238 (mp) cc_final: 0.7943 (tp) REVERT: O 36 GLN cc_start: 0.6521 (pt0) cc_final: 0.6142 (pt0) REVERT: O 39 LYS cc_start: 0.8086 (pttt) cc_final: 0.7763 (ptpt) REVERT: O 40 LEU cc_start: 0.7373 (tp) cc_final: 0.7062 (tp) REVERT: P 128 ARG cc_start: 0.6140 (mmt180) cc_final: 0.5566 (ttm-80) REVERT: Q 25 LEU cc_start: 0.4517 (mt) cc_final: 0.3921 (tp) REVERT: Q 27 ASP cc_start: 0.6752 (p0) cc_final: 0.6420 (m-30) REVERT: Q 28 MET cc_start: 0.6240 (mmm) cc_final: 0.5906 (mmm) REVERT: Q 31 GLU cc_start: 0.6254 (mp0) cc_final: 0.4495 (pm20) REVERT: Q 52 LYS cc_start: 0.4023 (mttm) cc_final: 0.3254 (tttp) REVERT: Q 93 MET cc_start: 0.1662 (tpp) cc_final: 0.1234 (tpt) REVERT: R 63 PHE cc_start: 0.4645 (m-80) cc_final: 0.4363 (m-80) REVERT: R 69 ARG cc_start: 0.6329 (mtp85) cc_final: 0.6014 (tmt170) REVERT: R 109 LYS cc_start: 0.6259 (pttt) cc_final: 0.5931 (mmmt) REVERT: S 34 VAL cc_start: 0.5734 (m) cc_final: 0.5392 (p) REVERT: S 81 ARG cc_start: 0.5200 (mtt-85) cc_final: 0.4855 (mtt180) REVERT: S 104 GLU cc_start: 0.4893 (pp20) cc_final: 0.3849 (tm-30) REVERT: S 107 LYS cc_start: 0.6956 (mmmm) cc_final: 0.6421 (tttt) REVERT: S 108 LEU cc_start: 0.6629 (pp) cc_final: 0.5628 (mt) REVERT: S 119 VAL cc_start: 0.7626 (t) cc_final: 0.7167 (p) REVERT: T 14 ARG cc_start: 0.4217 (mmm160) cc_final: 0.3766 (mmp80) REVERT: T 24 ARG cc_start: 0.2758 (mtt180) cc_final: 0.1855 (ptt90) REVERT: T 76 GLN cc_start: 0.6167 (mp10) cc_final: 0.5052 (tp-100) REVERT: T 109 GLU cc_start: 0.6412 (pp20) cc_final: 0.5886 (pp20) REVERT: U 22 LEU cc_start: 0.6828 (tp) cc_final: 0.6483 (mt) REVERT: U 54 TYR cc_start: 0.6407 (m-10) cc_final: 0.6031 (m-80) REVERT: U 63 HIS cc_start: 0.6940 (t70) cc_final: 0.5650 (t-170) REVERT: V 61 LEU cc_start: 0.6919 (tt) cc_final: 0.6694 (mt) REVERT: V 70 CYS cc_start: 0.7399 (t) cc_final: 0.7197 (t) REVERT: V 72 GLU cc_start: 0.4425 (pt0) cc_final: 0.3515 (mt-10) REVERT: V 77 TRP cc_start: 0.6870 (m100) cc_final: 0.6348 (m100) REVERT: V 78 ASP cc_start: 0.7233 (p0) cc_final: 0.6285 (p0) REVERT: V 79 ARG cc_start: 0.4717 (mtt-85) cc_final: 0.4283 (mtp85) REVERT: W 7 GLU cc_start: 0.5297 (mt-10) cc_final: 0.4848 (mt-10) REVERT: W 8 PHE cc_start: 0.7371 (m-10) cc_final: 0.7125 (m-10) REVERT: W 21 ASN cc_start: 0.6628 (t0) cc_final: 0.6008 (t0) REVERT: X 12 LYS cc_start: 0.6660 (tmmt) cc_final: 0.5950 (tppp) REVERT: X 36 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7875 (tpt170) REVERT: X 43 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7590 (mmmt) REVERT: X 56 HIS cc_start: 0.4196 (m170) cc_final: 0.3891 (m90) REVERT: X 88 LYS cc_start: 0.7391 (tptt) cc_final: 0.6863 (tppt) REVERT: X 119 LYS cc_start: 0.7231 (tttt) cc_final: 0.6743 (ttmm) REVERT: Y 14 ARG cc_start: 0.6104 (mmp80) cc_final: 0.5784 (mmm-85) REVERT: Y 52 LEU cc_start: 0.6105 (pp) cc_final: 0.4279 (tp) REVERT: Y 63 ASN cc_start: 0.7339 (p0) cc_final: 0.7077 (p0) REVERT: Y 130 LEU cc_start: 0.7296 (mm) cc_final: 0.6857 (pp) REVERT: Z 60 PHE cc_start: 0.2353 (m-80) cc_final: 0.2090 (m-80) REVERT: Z 64 PHE cc_start: 0.7274 (t80) cc_final: 0.6957 (t80) REVERT: Z 74 MET cc_start: 0.5222 (mmm) cc_final: 0.4599 (mmm) REVERT: Z 114 MET cc_start: 0.7777 (ttp) cc_final: 0.6769 (tmm) REVERT: b 52 ASP cc_start: 0.4756 (t0) cc_final: 0.4469 (m-30) REVERT: b 70 LYS cc_start: 0.5581 (tttt) cc_final: 0.5247 (tttp) REVERT: b 88 SER cc_start: 0.7713 (p) cc_final: 0.7436 (m) REVERT: b 94 ASP cc_start: 0.6588 (m-30) cc_final: 0.5848 (t0) REVERT: c 15 GLU cc_start: 0.7671 (mp0) cc_final: 0.7298 (mp0) REVERT: c 33 MET cc_start: 0.5861 (ptm) cc_final: 0.5442 (ptm) REVERT: c 34 ASP cc_start: 0.4747 (p0) cc_final: 0.4109 (p0) REVERT: c 40 CYS cc_start: 0.4005 (t) cc_final: 0.3228 (m) REVERT: c 65 GLN cc_start: 0.5793 (tt0) cc_final: 0.5581 (mp10) REVERT: c 80 ARG cc_start: 0.4593 (ptt90) cc_final: 0.3685 (ptp-170) REVERT: d 16 LYS cc_start: 0.3353 (tttt) cc_final: 0.2221 (mttt) REVERT: d 29 GLN cc_start: 0.5194 (mt0) cc_final: 0.4835 (mm110) REVERT: d 35 MET cc_start: 0.3921 (pmm) cc_final: 0.3669 (pmm) REVERT: e 13 LYS cc_start: 0.5079 (mtmt) cc_final: 0.4766 (mttm) REVERT: e 26 ASN cc_start: 0.5542 (t0) cc_final: 0.5307 (t0) REVERT: e 33 LYS cc_start: 0.6012 (tttt) cc_final: 0.5555 (mmmt) REVERT: e 41 GLN cc_start: 0.6121 (mt0) cc_final: 0.5871 (pm20) REVERT: f 131 ASN cc_start: 0.2856 (p0) cc_final: 0.2228 (p0) REVERT: h 5 MET cc_start: 0.0260 (pmm) cc_final: -0.0616 (tmm) REVERT: h 59 LEU cc_start: 0.2583 (mp) cc_final: 0.1850 (tp) REVERT: h 129 ILE cc_start: 0.3083 (mm) cc_final: 0.2700 (tp) REVERT: h 156 PHE cc_start: 0.3561 (m-10) cc_final: 0.3298 (p90) REVERT: h 265 ILE cc_start: 0.5556 (tp) cc_final: 0.5274 (mp) REVERT: n 10 MET cc_start: 0.7329 (tmm) cc_final: 0.7122 (tmm) REVERT: n 18 ARG cc_start: 0.3921 (ttm110) cc_final: 0.3106 (tpt170) REVERT: n 20 MET cc_start: 0.6798 (ppp) cc_final: 0.5875 (tpp) outliers start: 1 outliers final: 0 residues processed: 965 average time/residue: 0.8274 time to fit residues: 1311.6619 Evaluate side-chains 546 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 9.9990 chunk 499 optimal weight: 5.9990 chunk 277 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 336 optimal weight: 30.0000 chunk 266 optimal weight: 7.9990 chunk 516 optimal weight: 0.0870 chunk 199 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 384 optimal weight: 10.0000 chunk 598 optimal weight: 4.9990 overall best weight: 3.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN C 163 GLN C 202 GLN ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 179 GLN ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN I 165 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 12 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 44 HIS ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 16 HIS a 64 ASN e 37 ASN ** e 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 95 GLN ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 285 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 84105 Z= 0.174 Angle : 0.577 12.771 122449 Z= 0.289 Chirality : 0.034 0.255 15194 Planarity : 0.005 0.066 8634 Dihedral : 23.282 179.940 34536 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 0.14 % Allowed : 4.13 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.01 (0.11), residues: 4821 helix: -0.31 (0.13), residues: 1507 sheet: -1.26 (0.18), residues: 778 loop : -2.03 (0.11), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 90 HIS 0.016 0.001 HIS L 44 PHE 0.024 0.002 PHE E 11 TYR 0.020 0.001 TYR E 166 ARG 0.014 0.001 ARG V 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 679 time to evaluate : 4.421 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: B 10 MET cc_start: 0.5148 (mmm) cc_final: 0.4581 (mmt) REVERT: B 120 ARG cc_start: 0.5481 (mmm-85) cc_final: 0.4971 (mmm160) REVERT: B 135 THR cc_start: 0.7633 (p) cc_final: 0.7301 (t) REVERT: B 158 ASP cc_start: 0.5965 (m-30) cc_final: 0.5761 (t0) REVERT: B 195 TRP cc_start: 0.6153 (p-90) cc_final: 0.5652 (p-90) REVERT: C 87 ILE cc_start: 0.7384 (tt) cc_final: 0.6644 (pt) REVERT: C 103 MET cc_start: 0.6114 (tmm) cc_final: 0.5523 (tpp) REVERT: C 120 MET cc_start: 0.7271 (ttp) cc_final: 0.7009 (ttt) REVERT: D 65 LYS cc_start: 0.7082 (pttm) cc_final: 0.6594 (ptpt) REVERT: D 110 MET cc_start: 0.7296 (tpt) cc_final: 0.6956 (ttm) REVERT: D 176 LYS cc_start: 0.6877 (mttm) cc_final: 0.6230 (tptm) REVERT: D 212 LYS cc_start: 0.7380 (ptpp) cc_final: 0.6904 (ptmm) REVERT: D 266 TYR cc_start: 0.5321 (m-80) cc_final: 0.4823 (m-80) REVERT: E 1 MET cc_start: 0.0601 (ptt) cc_final: -0.0177 (tpp) REVERT: E 23 GLU cc_start: 0.6344 (tm-30) cc_final: 0.5525 (pt0) REVERT: E 174 HIS cc_start: 0.6876 (m-70) cc_final: 0.6325 (m170) REVERT: F 19 MET cc_start: 0.7112 (mmm) cc_final: 0.6492 (tpt) REVERT: F 125 LYS cc_start: 0.7388 (tttt) cc_final: 0.7113 (tttm) REVERT: F 127 ARG cc_start: 0.7046 (mmt90) cc_final: 0.6443 (ttm110) REVERT: F 182 MET cc_start: 0.8347 (tpt) cc_final: 0.8146 (tpt) REVERT: F 228 ILE cc_start: 0.8067 (pt) cc_final: 0.7806 (pt) REVERT: G 42 LYS cc_start: 0.5084 (mppt) cc_final: 0.4546 (tptm) REVERT: G 75 SER cc_start: 0.6168 (m) cc_final: 0.5901 (m) REVERT: G 77 MET cc_start: 0.3009 (mpp) cc_final: 0.2503 (mpp) REVERT: G 82 ASN cc_start: 0.3937 (m-40) cc_final: 0.3423 (t0) REVERT: G 166 ILE cc_start: 0.4549 (mt) cc_final: 0.3646 (mt) REVERT: H 52 ILE cc_start: 0.6174 (pt) cc_final: 0.5789 (pt) REVERT: H 217 MET cc_start: 0.5443 (mmm) cc_final: 0.5054 (mmm) REVERT: I 32 MET cc_start: 0.5547 (tpp) cc_final: 0.5261 (tpp) REVERT: I 73 GLN cc_start: 0.6882 (mp10) cc_final: 0.6394 (mm110) REVERT: I 127 ASP cc_start: 0.6740 (t0) cc_final: 0.6451 (t70) REVERT: I 131 GLU cc_start: 0.7035 (pp20) cc_final: 0.6811 (tm-30) REVERT: J 205 ARG cc_start: 0.6613 (tpt90) cc_final: 0.6313 (ttm-80) REVERT: K 27 GLN cc_start: 0.7437 (tp-100) cc_final: 0.6950 (tp-100) REVERT: K 45 ARG cc_start: 0.5491 (ttp-170) cc_final: 0.4853 (tmm-80) REVERT: K 66 LYS cc_start: 0.5909 (mmtt) cc_final: 0.4591 (ttmm) REVERT: K 108 ARG cc_start: 0.7771 (mmm160) cc_final: 0.6909 (tpp80) REVERT: K 147 PHE cc_start: 0.7428 (t80) cc_final: 0.7182 (t80) REVERT: K 152 ASP cc_start: 0.7531 (p0) cc_final: 0.7012 (m-30) REVERT: L 17 LYS cc_start: 0.7487 (mtmm) cc_final: 0.7002 (tptp) REVERT: L 45 VAL cc_start: 0.6750 (t) cc_final: 0.6338 (t) REVERT: M 95 TYR cc_start: 0.7277 (t80) cc_final: 0.6468 (t80) REVERT: M 103 GLU cc_start: 0.5534 (tp30) cc_final: 0.5285 (tp30) REVERT: M 118 ARG cc_start: 0.5625 (mtm-85) cc_final: 0.4628 (ttm110) REVERT: P 75 MET cc_start: 0.5295 (mmm) cc_final: 0.5023 (mmm) REVERT: P 128 ARG cc_start: 0.6314 (mmt180) cc_final: 0.5558 (ttm-80) REVERT: Q 25 LEU cc_start: 0.4638 (mt) cc_final: 0.4064 (tp) REVERT: Q 31 GLU cc_start: 0.6299 (mp0) cc_final: 0.5193 (pm20) REVERT: Q 32 GLN cc_start: 0.4737 (pp30) cc_final: 0.3995 (pp30) REVERT: Q 52 LYS cc_start: 0.3882 (mttm) cc_final: 0.3040 (ttmm) REVERT: Q 114 HIS cc_start: 0.4457 (m90) cc_final: 0.4250 (m-70) REVERT: R 63 PHE cc_start: 0.5120 (m-80) cc_final: 0.4798 (m-80) REVERT: R 69 ARG cc_start: 0.6419 (mtp85) cc_final: 0.5905 (tmt170) REVERT: R 109 LYS cc_start: 0.6025 (pttt) cc_final: 0.5717 (mmmt) REVERT: R 141 TYR cc_start: 0.6738 (m-10) cc_final: 0.6430 (m-80) REVERT: S 107 LYS cc_start: 0.7008 (mmmm) cc_final: 0.6515 (tttt) REVERT: S 108 LEU cc_start: 0.6572 (pp) cc_final: 0.6001 (mt) REVERT: T 24 ARG cc_start: 0.2857 (mtt180) cc_final: 0.2449 (mmt90) REVERT: T 76 GLN cc_start: 0.6070 (mp10) cc_final: 0.5198 (tp-100) REVERT: U 22 LEU cc_start: 0.6851 (tp) cc_final: 0.6381 (mt) REVERT: U 63 HIS cc_start: 0.6507 (t70) cc_final: 0.6085 (t-170) REVERT: V 61 LEU cc_start: 0.6178 (tt) cc_final: 0.5922 (mt) REVERT: V 70 CYS cc_start: 0.7681 (t) cc_final: 0.7086 (t) REVERT: V 72 GLU cc_start: 0.4786 (pt0) cc_final: 0.3987 (pt0) REVERT: V 77 TRP cc_start: 0.6938 (m100) cc_final: 0.6387 (m100) REVERT: V 78 ASP cc_start: 0.6534 (p0) cc_final: 0.6274 (p0) REVERT: W 7 GLU cc_start: 0.5415 (mt-10) cc_final: 0.5054 (mt-10) REVERT: W 21 ASN cc_start: 0.7039 (t0) cc_final: 0.6176 (t0) REVERT: X 12 LYS cc_start: 0.7107 (tmmt) cc_final: 0.6175 (tppp) REVERT: X 36 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7922 (mmt180) REVERT: X 44 HIS cc_start: 0.6347 (m-70) cc_final: 0.6061 (m170) REVERT: X 119 LYS cc_start: 0.7263 (tttt) cc_final: 0.6969 (ttmm) REVERT: Y 19 ASP cc_start: 0.5854 (m-30) cc_final: 0.5619 (m-30) REVERT: Y 52 LEU cc_start: 0.5555 (pp) cc_final: 0.5224 (tp) REVERT: Y 95 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6421 (mm-30) REVERT: Z 64 PHE cc_start: 0.7323 (t80) cc_final: 0.7100 (t80) REVERT: Z 114 MET cc_start: 0.7778 (ttp) cc_final: 0.6967 (tmm) REVERT: b 52 ASP cc_start: 0.5232 (t0) cc_final: 0.4574 (m-30) REVERT: b 88 SER cc_start: 0.7789 (p) cc_final: 0.7455 (m) REVERT: b 94 ASP cc_start: 0.6298 (m-30) cc_final: 0.5617 (t0) REVERT: c 15 GLU cc_start: 0.7741 (mp0) cc_final: 0.7430 (mp0) REVERT: c 26 GLN cc_start: 0.7104 (pm20) cc_final: 0.6708 (pt0) REVERT: c 40 CYS cc_start: 0.3519 (t) cc_final: 0.3227 (m) REVERT: c 65 GLN cc_start: 0.5972 (tt0) cc_final: 0.5764 (mm110) REVERT: c 80 ARG cc_start: 0.5088 (ptt90) cc_final: 0.4343 (ptp90) REVERT: d 16 LYS cc_start: 0.3706 (tttt) cc_final: 0.2466 (mttt) REVERT: d 51 ARG cc_start: 0.2270 (ttt180) cc_final: 0.1741 (ttt90) REVERT: e 26 ASN cc_start: 0.5525 (t0) cc_final: 0.5241 (t0) REVERT: f 117 ASN cc_start: 0.4610 (m-40) cc_final: 0.4355 (m-40) REVERT: h 5 MET cc_start: -0.0522 (pmm) cc_final: -0.1928 (ttp) REVERT: h 12 LYS cc_start: 0.2924 (pttt) cc_final: 0.2519 (pttp) REVERT: h 38 LYS cc_start: 0.2575 (mmpt) cc_final: 0.1948 (mtpt) REVERT: h 59 LEU cc_start: 0.2633 (mp) cc_final: 0.2418 (tp) REVERT: h 156 PHE cc_start: 0.3673 (m-10) cc_final: 0.3422 (p90) REVERT: h 265 ILE cc_start: 0.5498 (tp) cc_final: 0.5295 (mp) REVERT: n 1 MET cc_start: 0.6641 (tpt) cc_final: 0.6293 (tpt) REVERT: n 10 MET cc_start: 0.7471 (tmm) cc_final: 0.7224 (tmm) REVERT: n 18 ARG cc_start: 0.3980 (ttm110) cc_final: 0.3122 (tpt170) REVERT: n 20 MET cc_start: 0.6954 (ppp) cc_final: 0.5928 (tpp) outliers start: 6 outliers final: 3 residues processed: 685 average time/residue: 0.7909 time to fit residues: 907.7217 Evaluate side-chains 482 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 479 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 498 optimal weight: 0.7980 chunk 407 optimal weight: 30.0000 chunk 165 optimal weight: 30.0000 chunk 599 optimal weight: 0.4980 chunk 647 optimal weight: 20.0000 chunk 533 optimal weight: 0.0370 chunk 594 optimal weight: 0.4980 chunk 204 optimal weight: 7.9990 chunk 480 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 202 GLN ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS E 22 ASN I 91 HIS I 165 ASN J 9 HIS ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 120 HIS U 63 HIS V 100 GLN X 56 HIS Y 16 HIS Y 127 ASN b 17 HIS ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 191 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 84105 Z= 0.116 Angle : 0.502 9.383 122449 Z= 0.251 Chirality : 0.032 0.236 15194 Planarity : 0.004 0.055 8634 Dihedral : 23.168 179.597 34536 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.02 % Favored : 95.96 % Rotamer: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.53 (0.12), residues: 4821 helix: 0.32 (0.13), residues: 1502 sheet: -1.20 (0.19), residues: 734 loop : -1.82 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP h 43 HIS 0.007 0.001 HIS c 9 PHE 0.030 0.001 PHE G 97 TYR 0.037 0.001 TYR L 12 ARG 0.013 0.000 ARG e 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 680 time to evaluate : 4.452 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: B 120 ARG cc_start: 0.5406 (mmm-85) cc_final: 0.4910 (mmm160) REVERT: B 135 THR cc_start: 0.7913 (p) cc_final: 0.7425 (t) REVERT: C 34 LYS cc_start: 0.5464 (mmtt) cc_final: 0.5053 (mmmt) REVERT: C 103 MET cc_start: 0.6216 (tmm) cc_final: 0.5470 (tmm) REVERT: C 120 MET cc_start: 0.7301 (ttp) cc_final: 0.6126 (tmm) REVERT: D 65 LYS cc_start: 0.7087 (pttm) cc_final: 0.6801 (ptpt) REVERT: D 110 MET cc_start: 0.7253 (tpt) cc_final: 0.6943 (ttp) REVERT: D 176 LYS cc_start: 0.6870 (mttm) cc_final: 0.6215 (tptm) REVERT: D 212 LYS cc_start: 0.7306 (ptpp) cc_final: 0.6929 (ptmm) REVERT: D 254 ASP cc_start: 0.5930 (p0) cc_final: 0.5552 (p0) REVERT: D 266 TYR cc_start: 0.5186 (m-80) cc_final: 0.4568 (m-80) REVERT: E 1 MET cc_start: 0.1127 (ptt) cc_final: 0.0209 (tpt) REVERT: E 174 HIS cc_start: 0.6932 (m-70) cc_final: 0.6397 (m170) REVERT: F 19 MET cc_start: 0.6863 (mmm) cc_final: 0.6494 (tpt) REVERT: F 125 LYS cc_start: 0.7320 (tttt) cc_final: 0.7031 (tttm) REVERT: F 228 ILE cc_start: 0.7848 (pt) cc_final: 0.7581 (pt) REVERT: G 42 LYS cc_start: 0.4980 (mppt) cc_final: 0.4333 (tptm) REVERT: G 82 ASN cc_start: 0.3896 (m-40) cc_final: 0.3340 (t0) REVERT: G 122 ARG cc_start: 0.5589 (mmt90) cc_final: 0.5300 (mtp85) REVERT: G 171 GLU cc_start: 0.5660 (tp30) cc_final: 0.5447 (tp30) REVERT: H 1 MET cc_start: 0.7467 (ttt) cc_final: 0.6439 (tmm) REVERT: H 52 ILE cc_start: 0.6279 (pt) cc_final: 0.6031 (pt) REVERT: H 105 ASN cc_start: 0.7519 (t0) cc_final: 0.7263 (t0) REVERT: H 217 MET cc_start: 0.5563 (mmm) cc_final: 0.5121 (mmm) REVERT: I 32 MET cc_start: 0.5299 (tpp) cc_final: 0.5029 (tpp) REVERT: I 73 GLN cc_start: 0.6870 (mp10) cc_final: 0.6391 (mm110) REVERT: I 127 ASP cc_start: 0.6747 (t0) cc_final: 0.6363 (t70) REVERT: I 131 GLU cc_start: 0.7227 (pp20) cc_final: 0.6944 (tm-30) REVERT: J 174 CYS cc_start: 0.6705 (m) cc_final: 0.6389 (m) REVERT: J 205 ARG cc_start: 0.6643 (tpt90) cc_final: 0.6301 (ttm-80) REVERT: K 27 GLN cc_start: 0.7336 (tp-100) cc_final: 0.6977 (tp-100) REVERT: K 45 ARG cc_start: 0.5523 (ttp-170) cc_final: 0.4912 (tmm-80) REVERT: K 66 LYS cc_start: 0.5864 (mmtt) cc_final: 0.4690 (ttmm) REVERT: K 84 ILE cc_start: 0.7097 (mm) cc_final: 0.6824 (tt) REVERT: K 108 ARG cc_start: 0.7735 (mmm160) cc_final: 0.6776 (tpp80) REVERT: K 148 ILE cc_start: 0.8561 (mm) cc_final: 0.8012 (mm) REVERT: K 175 ARG cc_start: 0.6125 (ptt180) cc_final: 0.5125 (ptm160) REVERT: L 17 LYS cc_start: 0.7325 (mtmm) cc_final: 0.6879 (tptp) REVERT: L 35 LEU cc_start: 0.4110 (tt) cc_final: 0.3885 (mt) REVERT: M 118 ARG cc_start: 0.5597 (mtm-85) cc_final: 0.4558 (ttm110) REVERT: O 70 LYS cc_start: 0.7639 (ptpp) cc_final: 0.7176 (mtpt) REVERT: O 118 ILE cc_start: 0.8618 (pt) cc_final: 0.7989 (pt) REVERT: P 128 ARG cc_start: 0.6381 (mmt180) cc_final: 0.5560 (ttm-80) REVERT: Q 25 LEU cc_start: 0.4698 (mt) cc_final: 0.4116 (tp) REVERT: Q 31 GLU cc_start: 0.6558 (mp0) cc_final: 0.5044 (pm20) REVERT: Q 32 GLN cc_start: 0.4931 (pp30) cc_final: 0.4109 (pp30) REVERT: Q 52 LYS cc_start: 0.4040 (mttm) cc_final: 0.3162 (tttp) REVERT: R 63 PHE cc_start: 0.4757 (m-80) cc_final: 0.4188 (m-80) REVERT: R 69 ARG cc_start: 0.6245 (mtp85) cc_final: 0.5805 (tmt170) REVERT: R 109 LYS cc_start: 0.5990 (pttt) cc_final: 0.5723 (mmmt) REVERT: R 141 TYR cc_start: 0.6641 (m-10) cc_final: 0.6414 (m-80) REVERT: S 80 ARG cc_start: 0.4526 (mmt90) cc_final: 0.3715 (mtt-85) REVERT: S 81 ARG cc_start: 0.5361 (mtt-85) cc_final: 0.5111 (mtt180) REVERT: S 108 LEU cc_start: 0.6529 (pp) cc_final: 0.5932 (mt) REVERT: S 121 GLN cc_start: 0.6795 (pm20) cc_final: 0.6284 (mp10) REVERT: T 24 ARG cc_start: 0.2809 (mtt180) cc_final: 0.2413 (mmt90) REVERT: T 76 GLN cc_start: 0.6100 (mp10) cc_final: 0.5325 (tp-100) REVERT: U 22 LEU cc_start: 0.6775 (tp) cc_final: 0.6309 (mt) REVERT: V 68 THR cc_start: 0.8306 (p) cc_final: 0.8058 (t) REVERT: V 70 CYS cc_start: 0.8029 (t) cc_final: 0.6407 (m) REVERT: V 77 TRP cc_start: 0.7016 (m100) cc_final: 0.6472 (m100) REVERT: W 7 GLU cc_start: 0.5157 (mt-10) cc_final: 0.4822 (mt-10) REVERT: W 21 ASN cc_start: 0.7014 (t0) cc_final: 0.6090 (t0) REVERT: X 36 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7917 (mmt180) REVERT: X 111 MET cc_start: 0.6838 (ppp) cc_final: 0.6582 (ppp) REVERT: Y 27 TYR cc_start: 0.6266 (t80) cc_final: 0.5951 (t80) REVERT: Y 52 LEU cc_start: 0.5358 (pp) cc_final: 0.4958 (tp) REVERT: Z 80 ASP cc_start: 0.8009 (p0) cc_final: 0.7803 (p0) REVERT: Z 114 MET cc_start: 0.7693 (ttp) cc_final: 0.6734 (tmm) REVERT: b 52 ASP cc_start: 0.5094 (t0) cc_final: 0.4431 (m-30) REVERT: b 88 SER cc_start: 0.7671 (p) cc_final: 0.7223 (m) REVERT: b 94 ASP cc_start: 0.6419 (m-30) cc_final: 0.5681 (t0) REVERT: c 15 GLU cc_start: 0.7574 (mp0) cc_final: 0.7108 (mp0) REVERT: c 26 GLN cc_start: 0.6951 (pm20) cc_final: 0.6579 (pt0) REVERT: c 34 ASP cc_start: 0.5545 (p0) cc_final: 0.4981 (p0) REVERT: c 80 ARG cc_start: 0.5078 (ptt90) cc_final: 0.4169 (ptp-170) REVERT: d 16 LYS cc_start: 0.3682 (tttt) cc_final: 0.2390 (mttt) REVERT: d 51 ARG cc_start: 0.2264 (ttt180) cc_final: 0.1757 (ttt90) REVERT: e 26 ASN cc_start: 0.5370 (t0) cc_final: 0.5169 (t0) REVERT: e 36 LEU cc_start: 0.6577 (mt) cc_final: 0.6256 (mt) REVERT: f 117 ASN cc_start: 0.4583 (m-40) cc_final: 0.4352 (m-40) REVERT: h 5 MET cc_start: -0.0466 (pmm) cc_final: -0.1968 (ttp) REVERT: h 265 ILE cc_start: 0.5638 (tp) cc_final: 0.5414 (mp) REVERT: n 10 MET cc_start: 0.7325 (tmm) cc_final: 0.7115 (tmm) REVERT: n 18 ARG cc_start: 0.4007 (ttm110) cc_final: 0.3166 (tpt170) REVERT: n 20 MET cc_start: 0.6731 (ppp) cc_final: 0.5729 (tpp) outliers start: 2 outliers final: 0 residues processed: 680 average time/residue: 0.7852 time to fit residues: 894.1688 Evaluate side-chains 473 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 7.9990 chunk 450 optimal weight: 0.8980 chunk 311 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 402 optimal weight: 6.9990 chunk 601 optimal weight: 8.9990 chunk 636 optimal weight: 50.0000 chunk 314 optimal weight: 0.4980 chunk 570 optimal weight: 7.9990 chunk 171 optimal weight: 30.0000 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN C 101 HIS ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 272 HIS ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN K 113 GLN K 154 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 91 ASN e 37 ASN h 62 HIS ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 84105 Z= 0.225 Angle : 0.649 15.478 122449 Z= 0.325 Chirality : 0.037 0.315 15194 Planarity : 0.006 0.074 8634 Dihedral : 23.308 178.721 34536 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.06 % Favored : 93.92 % Rotamer: Outliers : 0.14 % Allowed : 5.17 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.50 (0.12), residues: 4821 helix: 0.43 (0.13), residues: 1487 sheet: -1.13 (0.19), residues: 718 loop : -1.85 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP J 67 HIS 0.008 0.001 HIS h 62 PHE 0.021 0.002 PHE T 28 TYR 0.039 0.002 TYR O 38 ARG 0.011 0.001 ARG h 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 598 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.5725 (tpp) cc_final: 0.4515 (tpp) REVERT: B 120 ARG cc_start: 0.5128 (mmm-85) cc_final: 0.4496 (mmm160) REVERT: B 195 TRP cc_start: 0.5723 (p-90) cc_final: 0.5153 (p-90) REVERT: C 103 MET cc_start: 0.6350 (tmm) cc_final: 0.5416 (tmm) REVERT: C 120 MET cc_start: 0.7070 (ttp) cc_final: 0.6321 (tmm) REVERT: C 183 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6756 (tm-30) REVERT: D 65 LYS cc_start: 0.7094 (pttm) cc_final: 0.6602 (ptpt) REVERT: D 83 LEU cc_start: 0.8014 (mt) cc_final: 0.7638 (mt) REVERT: D 110 MET cc_start: 0.7261 (tpt) cc_final: 0.6972 (ttp) REVERT: E 1 MET cc_start: 0.1217 (ptt) cc_final: -0.0327 (tpp) REVERT: E 23 GLU cc_start: 0.5524 (tm-30) cc_final: 0.5286 (tm-30) REVERT: E 41 VAL cc_start: 0.2942 (m) cc_final: 0.2669 (p) REVERT: E 174 HIS cc_start: 0.6664 (m-70) cc_final: 0.6366 (m90) REVERT: F 19 MET cc_start: 0.7513 (mmm) cc_final: 0.7301 (mmm) REVERT: F 127 ARG cc_start: 0.7164 (mmt90) cc_final: 0.6349 (ttm110) REVERT: G 42 LYS cc_start: 0.4860 (mppt) cc_final: 0.4459 (tptm) REVERT: G 201 LYS cc_start: 0.3927 (mttm) cc_final: 0.3692 (mmtm) REVERT: H 52 ILE cc_start: 0.6540 (pt) cc_final: 0.6331 (pt) REVERT: H 105 ASN cc_start: 0.7536 (t0) cc_final: 0.7332 (t0) REVERT: H 224 ARG cc_start: 0.4275 (ptp-170) cc_final: 0.3759 (ttp80) REVERT: I 127 ASP cc_start: 0.6673 (t0) cc_final: 0.6346 (t70) REVERT: I 131 GLU cc_start: 0.7463 (pp20) cc_final: 0.7124 (tm-30) REVERT: I 157 HIS cc_start: 0.6798 (m90) cc_final: 0.6524 (m90) REVERT: I 186 ASN cc_start: 0.7273 (m-40) cc_final: 0.6871 (m-40) REVERT: J 109 TYR cc_start: 0.5986 (m-80) cc_final: 0.5777 (m-80) REVERT: J 174 CYS cc_start: 0.7061 (m) cc_final: 0.6812 (m) REVERT: J 205 ARG cc_start: 0.6780 (tpt90) cc_final: 0.6361 (ttm-80) REVERT: K 27 GLN cc_start: 0.7258 (tp-100) cc_final: 0.6997 (tp-100) REVERT: K 45 ARG cc_start: 0.5440 (ttp-170) cc_final: 0.4704 (tmm-80) REVERT: K 53 ILE cc_start: 0.7302 (mt) cc_final: 0.7093 (tt) REVERT: K 66 LYS cc_start: 0.6148 (mmtt) cc_final: 0.4692 (ttmm) REVERT: K 84 ILE cc_start: 0.7336 (mm) cc_final: 0.6912 (tt) REVERT: K 104 ASP cc_start: 0.6672 (m-30) cc_final: 0.6417 (t0) REVERT: K 175 ARG cc_start: 0.6222 (ptt180) cc_final: 0.5230 (ptm160) REVERT: L 12 TYR cc_start: 0.5164 (m-80) cc_final: 0.4816 (m-80) REVERT: M 95 TYR cc_start: 0.7161 (t80) cc_final: 0.6939 (t80) REVERT: M 118 ARG cc_start: 0.5638 (mtm-85) cc_final: 0.4664 (ttm110) REVERT: N 101 ARG cc_start: 0.1994 (ptt90) cc_final: 0.1339 (ptt90) REVERT: O 16 LEU cc_start: 0.8124 (mp) cc_final: 0.7812 (tp) REVERT: P 128 ARG cc_start: 0.6493 (mmt180) cc_final: 0.5782 (tpp-160) REVERT: Q 31 GLU cc_start: 0.6780 (mp0) cc_final: 0.5044 (pm20) REVERT: Q 52 LYS cc_start: 0.4121 (mttm) cc_final: 0.3107 (tttp) REVERT: Q 118 GLU cc_start: 0.4925 (tt0) cc_final: 0.3919 (mp0) REVERT: R 63 PHE cc_start: 0.5124 (m-80) cc_final: 0.4856 (m-80) REVERT: R 69 ARG cc_start: 0.6481 (mtp85) cc_final: 0.5805 (tmt170) REVERT: R 109 LYS cc_start: 0.6140 (pttt) cc_final: 0.5828 (mmmt) REVERT: R 141 TYR cc_start: 0.7021 (m-10) cc_final: 0.6652 (m-80) REVERT: S 96 ILE cc_start: 0.3754 (mm) cc_final: 0.3395 (mt) REVERT: S 108 LEU cc_start: 0.6456 (pp) cc_final: 0.6031 (mt) REVERT: T 17 ASN cc_start: 0.3732 (p0) cc_final: 0.3131 (p0) REVERT: T 24 ARG cc_start: 0.2683 (mtt180) cc_final: 0.2261 (mmt90) REVERT: T 76 GLN cc_start: 0.6209 (mp10) cc_final: 0.5346 (tp-100) REVERT: U 22 LEU cc_start: 0.6655 (tp) cc_final: 0.6153 (mt) REVERT: U 75 MET cc_start: 0.8412 (mpp) cc_final: 0.7742 (mmp) REVERT: V 77 TRP cc_start: 0.6857 (m100) cc_final: 0.6317 (m100) REVERT: V 78 ASP cc_start: 0.6704 (p0) cc_final: 0.6464 (p0) REVERT: W 15 ARG cc_start: 0.5529 (mtp180) cc_final: 0.5193 (mtm180) REVERT: X 12 LYS cc_start: 0.7401 (tmmt) cc_final: 0.6391 (tppp) REVERT: X 36 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7902 (mmt180) REVERT: X 51 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6314 (mm-30) REVERT: X 88 LYS cc_start: 0.7483 (tptt) cc_final: 0.6631 (tptp) REVERT: Y 25 LYS cc_start: 0.6193 (ttmt) cc_final: 0.5463 (tptt) REVERT: Y 27 TYR cc_start: 0.6344 (t80) cc_final: 0.5946 (t80) REVERT: Y 95 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6308 (mm-30) REVERT: Z 80 ASP cc_start: 0.8056 (p0) cc_final: 0.7742 (p0) REVERT: b 36 ILE cc_start: 0.6857 (mt) cc_final: 0.6552 (mt) REVERT: b 52 ASP cc_start: 0.5536 (t0) cc_final: 0.5094 (t0) REVERT: b 88 SER cc_start: 0.7601 (p) cc_final: 0.7147 (m) REVERT: c 15 GLU cc_start: 0.7778 (mp0) cc_final: 0.7157 (mp0) REVERT: c 34 ASP cc_start: 0.6284 (p0) cc_final: 0.5781 (p0) REVERT: c 72 ARG cc_start: 0.6291 (tpp80) cc_final: 0.6053 (tpp-160) REVERT: c 80 ARG cc_start: 0.5749 (ptt90) cc_final: 0.4349 (ptp-170) REVERT: d 16 LYS cc_start: 0.4030 (tttt) cc_final: 0.1489 (mttt) REVERT: d 31 ARG cc_start: 0.5495 (tpm170) cc_final: 0.5122 (mtm180) REVERT: h 113 PHE cc_start: 0.1271 (m-80) cc_final: 0.0916 (m-80) REVERT: h 265 ILE cc_start: 0.5786 (tp) cc_final: 0.5535 (mp) REVERT: n 18 ARG cc_start: 0.3943 (ttm110) cc_final: 0.3216 (tpt170) REVERT: n 20 MET cc_start: 0.6904 (ppp) cc_final: 0.5831 (tpp) outliers start: 6 outliers final: 2 residues processed: 604 average time/residue: 0.8079 time to fit residues: 827.6612 Evaluate side-chains 426 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 424 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 530 optimal weight: 6.9990 chunk 361 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 0.3980 chunk 262 optimal weight: 4.9990 chunk 543 optimal weight: 30.0000 chunk 440 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 6.9990 chunk 571 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 overall best weight: 3.8824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN C 101 HIS ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN I 126 HIS I 165 ASN ** J 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS R 11 GLN U 12 GLN U 83 GLN ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 41 GLN ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 84105 Z= 0.166 Angle : 0.569 11.772 122449 Z= 0.283 Chirality : 0.034 0.228 15194 Planarity : 0.004 0.079 8634 Dihedral : 23.255 179.198 34536 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.35 (0.12), residues: 4821 helix: 0.65 (0.13), residues: 1479 sheet: -1.18 (0.18), residues: 767 loop : -1.78 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP h 170 HIS 0.004 0.001 HIS Z 29 PHE 0.035 0.002 PHE L 16 TYR 0.043 0.002 TYR O 38 ARG 0.007 0.001 ARG e 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 585 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.5797 (tpp) cc_final: 0.4681 (tpp) REVERT: B 120 ARG cc_start: 0.5105 (mmm-85) cc_final: 0.4623 (mmm160) REVERT: B 195 TRP cc_start: 0.5924 (p-90) cc_final: 0.5453 (p-90) REVERT: C 34 LYS cc_start: 0.5337 (mmtt) cc_final: 0.4907 (mmmt) REVERT: C 103 MET cc_start: 0.6334 (tmm) cc_final: 0.5445 (tmm) REVERT: C 120 MET cc_start: 0.7204 (ttp) cc_final: 0.6934 (ttp) REVERT: C 183 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6738 (tm-30) REVERT: D 65 LYS cc_start: 0.7061 (pttm) cc_final: 0.6482 (ptpt) REVERT: D 83 LEU cc_start: 0.7901 (mt) cc_final: 0.7616 (mt) REVERT: D 110 MET cc_start: 0.7271 (tpt) cc_final: 0.7023 (ttp) REVERT: D 173 LYS cc_start: 0.6455 (ttmt) cc_final: 0.5717 (mmtp) REVERT: D 225 SER cc_start: 0.7210 (t) cc_final: 0.6895 (p) REVERT: E 1 MET cc_start: 0.1159 (ptt) cc_final: 0.0110 (tpp) REVERT: E 41 VAL cc_start: 0.3179 (m) cc_final: 0.2862 (p) REVERT: E 174 HIS cc_start: 0.6676 (m-70) cc_final: 0.6282 (m90) REVERT: F 66 MET cc_start: 0.4214 (ttp) cc_final: 0.3680 (ttp) REVERT: F 127 ARG cc_start: 0.7118 (mmt90) cc_final: 0.6892 (mtt-85) REVERT: G 42 LYS cc_start: 0.4752 (mppt) cc_final: 0.4362 (tptm) REVERT: G 201 LYS cc_start: 0.4293 (mttm) cc_final: 0.4048 (mmtm) REVERT: H 105 ASN cc_start: 0.7445 (t0) cc_final: 0.7223 (t0) REVERT: I 73 GLN cc_start: 0.6614 (mp10) cc_final: 0.6243 (mm110) REVERT: I 127 ASP cc_start: 0.6611 (t0) cc_final: 0.6404 (t70) REVERT: I 131 GLU cc_start: 0.7379 (pp20) cc_final: 0.7046 (tm-30) REVERT: I 157 HIS cc_start: 0.6769 (m90) cc_final: 0.6497 (m90) REVERT: I 186 ASN cc_start: 0.7147 (m-40) cc_final: 0.6745 (m-40) REVERT: J 109 TYR cc_start: 0.6070 (m-80) cc_final: 0.5806 (m-80) REVERT: J 174 CYS cc_start: 0.7074 (m) cc_final: 0.6744 (m) REVERT: J 205 ARG cc_start: 0.6835 (tpt90) cc_final: 0.6369 (ttm-80) REVERT: K 45 ARG cc_start: 0.5470 (ttp-170) cc_final: 0.4504 (tmm-80) REVERT: K 53 ILE cc_start: 0.7388 (mt) cc_final: 0.7143 (tt) REVERT: K 66 LYS cc_start: 0.6118 (mmtt) cc_final: 0.4703 (ttmm) REVERT: K 84 ILE cc_start: 0.7410 (mm) cc_final: 0.6993 (tt) REVERT: K 104 ASP cc_start: 0.6746 (m-30) cc_final: 0.6513 (t0) REVERT: K 148 ILE cc_start: 0.8822 (mm) cc_final: 0.8546 (mt) REVERT: K 175 ARG cc_start: 0.6155 (ptt180) cc_final: 0.5195 (ptm160) REVERT: M 49 GLU cc_start: 0.5798 (tm-30) cc_final: 0.5533 (tm-30) REVERT: M 95 TYR cc_start: 0.7151 (t80) cc_final: 0.6850 (t80) REVERT: M 118 ARG cc_start: 0.5492 (mtm-85) cc_final: 0.4503 (ttm110) REVERT: P 30 VAL cc_start: 0.7496 (p) cc_final: 0.7270 (p) REVERT: P 128 ARG cc_start: 0.6547 (mmt180) cc_final: 0.5807 (tpp-160) REVERT: Q 25 LEU cc_start: 0.4562 (mt) cc_final: 0.4348 (tp) REVERT: Q 31 GLU cc_start: 0.6468 (mp0) cc_final: 0.5171 (pm20) REVERT: R 63 PHE cc_start: 0.5164 (m-80) cc_final: 0.4904 (m-80) REVERT: R 69 ARG cc_start: 0.6403 (mtp85) cc_final: 0.5785 (tmt170) REVERT: R 109 LYS cc_start: 0.6366 (pttt) cc_final: 0.6031 (mmmt) REVERT: S 21 TYR cc_start: 0.5881 (t80) cc_final: 0.5629 (t80) REVERT: S 108 LEU cc_start: 0.6458 (pp) cc_final: 0.5797 (mp) REVERT: S 121 GLN cc_start: 0.6911 (pm20) cc_final: 0.6480 (mp10) REVERT: T 17 ASN cc_start: 0.3776 (p0) cc_final: 0.3197 (p0) REVERT: T 24 ARG cc_start: 0.2598 (mtt180) cc_final: 0.2328 (mmt90) REVERT: T 76 GLN cc_start: 0.6284 (mp10) cc_final: 0.5465 (tp-100) REVERT: U 22 LEU cc_start: 0.6370 (tp) cc_final: 0.6047 (mt) REVERT: U 75 MET cc_start: 0.8576 (mpp) cc_final: 0.7814 (mmp) REVERT: U 78 ILE cc_start: 0.6403 (pt) cc_final: 0.5002 (pt) REVERT: V 70 CYS cc_start: 0.7838 (t) cc_final: 0.7474 (t) REVERT: V 72 GLU cc_start: 0.4997 (pp20) cc_final: 0.4794 (tm-30) REVERT: V 77 TRP cc_start: 0.6810 (m100) cc_final: 0.6379 (m100) REVERT: V 78 ASP cc_start: 0.6553 (p0) cc_final: 0.6322 (p0) REVERT: X 36 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7912 (mmt180) REVERT: X 40 VAL cc_start: 0.8146 (p) cc_final: 0.7853 (m) REVERT: X 51 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6496 (mm-30) REVERT: X 88 LYS cc_start: 0.7283 (tptt) cc_final: 0.6453 (tptp) REVERT: X 103 VAL cc_start: 0.8422 (m) cc_final: 0.8192 (m) REVERT: Y 25 LYS cc_start: 0.6155 (ttmt) cc_final: 0.5539 (tptt) REVERT: Y 27 TYR cc_start: 0.6092 (t80) cc_final: 0.5874 (t80) REVERT: Y 95 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6184 (mm-30) REVERT: Y 140 ARG cc_start: 0.6501 (tmt170) cc_final: 0.6134 (ptm160) REVERT: Z 80 ASP cc_start: 0.8120 (p0) cc_final: 0.7885 (p0) REVERT: Z 109 GLU cc_start: 0.7467 (mp0) cc_final: 0.7198 (mp0) REVERT: Z 114 MET cc_start: 0.7579 (ttp) cc_final: 0.6934 (tmm) REVERT: b 36 ILE cc_start: 0.6841 (mt) cc_final: 0.6609 (mt) REVERT: b 52 ASP cc_start: 0.5368 (t0) cc_final: 0.5027 (t0) REVERT: b 88 SER cc_start: 0.7430 (p) cc_final: 0.6841 (m) REVERT: b 94 ASP cc_start: 0.6303 (m-30) cc_final: 0.5375 (t0) REVERT: c 15 GLU cc_start: 0.7698 (mp0) cc_final: 0.7084 (mp0) REVERT: c 34 ASP cc_start: 0.6291 (p0) cc_final: 0.5926 (p0) REVERT: d 16 LYS cc_start: 0.4137 (tttt) cc_final: 0.1721 (mttt) REVERT: d 31 ARG cc_start: 0.5679 (tpm170) cc_final: 0.5201 (mtm180) REVERT: e 36 LEU cc_start: 0.5814 (mm) cc_final: 0.5593 (mt) REVERT: h 77 PHE cc_start: 0.4722 (m-80) cc_final: 0.4491 (m-80) REVERT: h 113 PHE cc_start: 0.1153 (m-80) cc_final: 0.0916 (m-80) REVERT: h 265 ILE cc_start: 0.5794 (tp) cc_final: 0.5555 (mp) REVERT: n 18 ARG cc_start: 0.3970 (ttm110) cc_final: 0.3125 (tpt170) REVERT: n 20 MET cc_start: 0.6799 (ppp) cc_final: 0.5795 (tpp) outliers start: 4 outliers final: 1 residues processed: 587 average time/residue: 0.7675 time to fit residues: 763.3899 Evaluate side-chains 420 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 419 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 214 optimal weight: 7.9990 chunk 573 optimal weight: 8.9990 chunk 125 optimal weight: 30.0000 chunk 373 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 chunk 637 optimal weight: 10.0000 chunk 529 optimal weight: 20.0000 chunk 295 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 6.9990 chunk 334 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN D 113 GLN D 272 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN I 165 ASN J 22 HIS K 154 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN b 7 ASN e 41 GLN ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 84105 Z= 0.281 Angle : 0.735 17.940 122449 Z= 0.365 Chirality : 0.040 0.317 15194 Planarity : 0.006 0.072 8634 Dihedral : 23.546 177.156 34536 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.88 % Favored : 92.10 % Rotamer: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.85 (0.11), residues: 4821 helix: 0.07 (0.13), residues: 1496 sheet: -1.38 (0.18), residues: 764 loop : -2.01 (0.12), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP h 90 HIS 0.017 0.002 HIS G 79 PHE 0.030 0.003 PHE Z 60 TYR 0.042 0.003 TYR O 38 ARG 0.013 0.001 ARG Q 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 545 time to evaluate : 4.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ARG cc_start: 0.4984 (mmm-85) cc_final: 0.4365 (mmm160) REVERT: B 195 TRP cc_start: 0.5757 (p-90) cc_final: 0.5254 (p-90) REVERT: C 103 MET cc_start: 0.6559 (tmm) cc_final: 0.6051 (tmm) REVERT: C 120 MET cc_start: 0.6766 (ttp) cc_final: 0.6535 (ttt) REVERT: C 175 GLU cc_start: 0.6306 (mm-30) cc_final: 0.6002 (tp30) REVERT: C 183 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6757 (tm-30) REVERT: D 65 LYS cc_start: 0.7068 (pttm) cc_final: 0.6513 (ptpt) REVERT: D 83 LEU cc_start: 0.7838 (mt) cc_final: 0.7297 (mt) REVERT: D 225 SER cc_start: 0.7380 (t) cc_final: 0.7058 (p) REVERT: E 1 MET cc_start: 0.1301 (ptt) cc_final: -0.0229 (tpp) REVERT: E 41 VAL cc_start: 0.3260 (m) cc_final: 0.2960 (p) REVERT: E 174 HIS cc_start: 0.6699 (m-70) cc_final: 0.6388 (m90) REVERT: F 127 ARG cc_start: 0.7158 (mmt90) cc_final: 0.6851 (mmt180) REVERT: G 42 LYS cc_start: 0.4585 (mppt) cc_final: 0.4216 (tptm) REVERT: G 76 MET cc_start: 0.5604 (mmm) cc_final: 0.5356 (mmp) REVERT: H 52 ILE cc_start: 0.6252 (pt) cc_final: 0.6020 (pt) REVERT: H 105 ASN cc_start: 0.7353 (t0) cc_final: 0.7078 (t0) REVERT: I 127 ASP cc_start: 0.6721 (t0) cc_final: 0.6428 (t70) REVERT: I 131 GLU cc_start: 0.7390 (pp20) cc_final: 0.7117 (tm-30) REVERT: J 109 TYR cc_start: 0.6134 (m-80) cc_final: 0.5913 (m-80) REVERT: J 174 CYS cc_start: 0.6987 (m) cc_final: 0.6727 (m) REVERT: J 205 ARG cc_start: 0.6913 (tpt90) cc_final: 0.6388 (ttm-80) REVERT: K 45 ARG cc_start: 0.5282 (ttp-170) cc_final: 0.4989 (tmm-80) REVERT: K 66 LYS cc_start: 0.6115 (mmtt) cc_final: 0.4471 (ttmm) REVERT: K 104 ASP cc_start: 0.7152 (m-30) cc_final: 0.6657 (t0) REVERT: K 175 ARG cc_start: 0.6202 (ptt180) cc_final: 0.5246 (ptm160) REVERT: L 13 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6125 (mm-30) REVERT: M 74 SER cc_start: 0.6565 (m) cc_final: 0.6134 (p) REVERT: M 95 TYR cc_start: 0.7336 (t80) cc_final: 0.6916 (t80) REVERT: M 118 ARG cc_start: 0.5277 (mtm-85) cc_final: 0.4750 (ttm110) REVERT: O 9 LYS cc_start: 0.6466 (ttpt) cc_final: 0.5943 (ttpp) REVERT: O 133 ARG cc_start: 0.7223 (tpm170) cc_final: 0.6930 (tpm170) REVERT: P 128 ARG cc_start: 0.6250 (mmt180) cc_final: 0.5355 (tpp-160) REVERT: Q 25 LEU cc_start: 0.4290 (mt) cc_final: 0.3908 (tp) REVERT: Q 31 GLU cc_start: 0.6272 (mp0) cc_final: 0.5202 (pm20) REVERT: R 63 PHE cc_start: 0.5081 (m-80) cc_final: 0.4800 (m-80) REVERT: S 108 LEU cc_start: 0.6482 (pp) cc_final: 0.5956 (mt) REVERT: T 24 ARG cc_start: 0.2059 (mtt180) cc_final: 0.1331 (tpt-90) REVERT: T 76 GLN cc_start: 0.6449 (mp10) cc_final: 0.5700 (tp-100) REVERT: U 22 LEU cc_start: 0.6242 (tp) cc_final: 0.5967 (mt) REVERT: U 75 MET cc_start: 0.8621 (mpp) cc_final: 0.7915 (mmp) REVERT: V 77 TRP cc_start: 0.6872 (m100) cc_final: 0.6374 (m100) REVERT: V 78 ASP cc_start: 0.6688 (p0) cc_final: 0.6390 (p0) REVERT: W 15 ARG cc_start: 0.5316 (mtp180) cc_final: 0.4923 (mtm180) REVERT: X 40 VAL cc_start: 0.8184 (p) cc_final: 0.7799 (m) REVERT: Y 25 LYS cc_start: 0.5950 (ttmt) cc_final: 0.5181 (tttm) REVERT: Y 27 TYR cc_start: 0.6523 (t80) cc_final: 0.6042 (t80) REVERT: Z 114 MET cc_start: 0.7593 (ttp) cc_final: 0.6858 (tmt) REVERT: b 52 ASP cc_start: 0.5565 (t0) cc_final: 0.5299 (t0) REVERT: b 88 SER cc_start: 0.7498 (p) cc_final: 0.6782 (m) REVERT: b 100 ARG cc_start: 0.3325 (ttp-170) cc_final: 0.2367 (tmm-80) REVERT: c 8 LEU cc_start: 0.5413 (mt) cc_final: 0.5146 (mm) REVERT: c 15 GLU cc_start: 0.7885 (mp0) cc_final: 0.7343 (mp0) REVERT: d 16 LYS cc_start: 0.3943 (tttt) cc_final: 0.1622 (mttt) REVERT: d 31 ARG cc_start: 0.6060 (tpm170) cc_final: 0.5325 (mtm180) REVERT: e 36 LEU cc_start: 0.5600 (mm) cc_final: 0.5285 (mt) REVERT: e 38 MET cc_start: 0.7140 (ttt) cc_final: 0.6791 (ttt) REVERT: f 82 VAL cc_start: 0.8609 (m) cc_final: 0.8344 (m) REVERT: h 77 PHE cc_start: 0.4944 (m-80) cc_final: 0.4616 (m-10) REVERT: h 234 ASP cc_start: 0.3556 (t0) cc_final: 0.2129 (m-30) REVERT: n 18 ARG cc_start: 0.3817 (ttm110) cc_final: 0.3087 (tpt170) REVERT: n 20 MET cc_start: 0.7002 (ppp) cc_final: 0.6048 (tpp) outliers start: 2 outliers final: 0 residues processed: 547 average time/residue: 0.7738 time to fit residues: 718.1946 Evaluate side-chains 407 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 5.9990 chunk 465 optimal weight: 0.0570 chunk 360 optimal weight: 5.9990 chunk 536 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 635 optimal weight: 20.0000 chunk 397 optimal weight: 10.0000 chunk 387 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN I 162 GLN ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 12 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 ASN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 84105 Z= 0.207 Angle : 0.637 14.306 122449 Z= 0.318 Chirality : 0.037 0.259 15194 Planarity : 0.005 0.066 8634 Dihedral : 23.475 178.120 34536 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.29 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.71 (0.12), residues: 4821 helix: 0.26 (0.13), residues: 1491 sheet: -1.31 (0.18), residues: 761 loop : -1.98 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 64 HIS 0.014 0.001 HIS g 135 PHE 0.027 0.002 PHE G 97 TYR 0.047 0.002 TYR O 38 ARG 0.011 0.001 ARG M 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 4.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.5637 (tpp) cc_final: 0.4621 (tpp) REVERT: B 120 ARG cc_start: 0.4827 (mmm-85) cc_final: 0.4488 (mmm160) REVERT: B 195 TRP cc_start: 0.5766 (p-90) cc_final: 0.5356 (p-90) REVERT: C 34 LYS cc_start: 0.5059 (mmtt) cc_final: 0.4582 (mmmt) REVERT: C 103 MET cc_start: 0.6445 (tmm) cc_final: 0.5986 (tmm) REVERT: C 175 GLU cc_start: 0.6250 (mm-30) cc_final: 0.5972 (tp30) REVERT: C 183 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6654 (tm-30) REVERT: D 65 LYS cc_start: 0.7168 (pttm) cc_final: 0.6663 (ptpt) REVERT: D 83 LEU cc_start: 0.7844 (mt) cc_final: 0.7272 (mt) REVERT: D 225 SER cc_start: 0.7438 (t) cc_final: 0.7169 (p) REVERT: E 1 MET cc_start: 0.1404 (ptt) cc_final: -0.0275 (tpt) REVERT: E 23 GLU cc_start: 0.5489 (tm-30) cc_final: 0.5116 (tm-30) REVERT: E 41 VAL cc_start: 0.3224 (m) cc_final: 0.2934 (p) REVERT: G 42 LYS cc_start: 0.4714 (mppt) cc_final: 0.4366 (tptm) REVERT: H 52 ILE cc_start: 0.6222 (pt) cc_final: 0.6006 (pt) REVERT: H 105 ASN cc_start: 0.7282 (t0) cc_final: 0.6964 (t0) REVERT: I 32 MET cc_start: 0.5464 (tpp) cc_final: 0.5214 (tpp) REVERT: I 127 ASP cc_start: 0.6651 (t0) cc_final: 0.6273 (t70) REVERT: I 131 GLU cc_start: 0.7264 (pp20) cc_final: 0.6960 (tm-30) REVERT: I 157 HIS cc_start: 0.6939 (m-70) cc_final: 0.6185 (m90) REVERT: J 94 LYS cc_start: 0.5710 (mmtp) cc_final: 0.5151 (mttp) REVERT: J 109 TYR cc_start: 0.6247 (m-80) cc_final: 0.6014 (m-80) REVERT: J 174 CYS cc_start: 0.7058 (m) cc_final: 0.6734 (m) REVERT: J 205 ARG cc_start: 0.6920 (tpt90) cc_final: 0.6313 (ttm-80) REVERT: K 45 ARG cc_start: 0.5308 (ttp-170) cc_final: 0.5012 (tmm-80) REVERT: K 84 ILE cc_start: 0.7545 (mm) cc_final: 0.7247 (tt) REVERT: K 104 ASP cc_start: 0.7066 (m-30) cc_final: 0.6526 (t0) REVERT: K 148 ILE cc_start: 0.8878 (mm) cc_final: 0.8677 (mt) REVERT: K 175 ARG cc_start: 0.6317 (ptt180) cc_final: 0.5373 (ptm160) REVERT: L 1 MET cc_start: 0.3366 (tpt) cc_final: 0.2819 (tpp) REVERT: L 12 TYR cc_start: 0.5047 (m-80) cc_final: 0.4846 (m-80) REVERT: L 13 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6279 (mm-30) REVERT: M 95 TYR cc_start: 0.7227 (t80) cc_final: 0.6921 (t80) REVERT: O 9 LYS cc_start: 0.6465 (ttpt) cc_final: 0.5988 (ttpp) REVERT: O 133 ARG cc_start: 0.7180 (tpm170) cc_final: 0.6862 (tpm170) REVERT: P 128 ARG cc_start: 0.6347 (mmt180) cc_final: 0.5425 (tpp-160) REVERT: Q 25 LEU cc_start: 0.4190 (mt) cc_final: 0.3782 (tp) REVERT: Q 31 GLU cc_start: 0.6277 (mp0) cc_final: 0.4935 (pm20) REVERT: Q 88 GLU cc_start: 0.5023 (tm-30) cc_final: 0.4732 (tm-30) REVERT: R 63 PHE cc_start: 0.5287 (m-80) cc_final: 0.5043 (m-80) REVERT: R 109 LYS cc_start: 0.6580 (pttt) cc_final: 0.6177 (mmmt) REVERT: S 108 LEU cc_start: 0.6425 (pp) cc_final: 0.5910 (mp) REVERT: S 121 GLN cc_start: 0.6857 (pm20) cc_final: 0.6484 (mp10) REVERT: T 24 ARG cc_start: 0.2197 (mtt180) cc_final: 0.1415 (tpt-90) REVERT: T 76 GLN cc_start: 0.6581 (mp10) cc_final: 0.5862 (tp-100) REVERT: U 75 MET cc_start: 0.8602 (mpp) cc_final: 0.7890 (mmp) REVERT: U 78 ILE cc_start: 0.6484 (pt) cc_final: 0.5321 (pt) REVERT: V 77 TRP cc_start: 0.6899 (m100) cc_final: 0.6477 (m100) REVERT: V 78 ASP cc_start: 0.6588 (p0) cc_final: 0.6259 (p0) REVERT: W 15 ARG cc_start: 0.5231 (mtp180) cc_final: 0.4860 (mtm180) REVERT: X 12 LYS cc_start: 0.7135 (tmmt) cc_final: 0.6157 (tppp) REVERT: X 40 VAL cc_start: 0.8086 (p) cc_final: 0.7733 (m) REVERT: X 88 LYS cc_start: 0.6963 (tptt) cc_final: 0.6341 (tptp) REVERT: Y 25 LYS cc_start: 0.5725 (ttmt) cc_final: 0.4857 (tttm) REVERT: Y 27 TYR cc_start: 0.6200 (t80) cc_final: 0.5952 (t80) REVERT: Z 114 MET cc_start: 0.7557 (ttp) cc_final: 0.6882 (tmt) REVERT: b 85 ARG cc_start: 0.6716 (ptp-110) cc_final: 0.6482 (mtp180) REVERT: b 88 SER cc_start: 0.7246 (p) cc_final: 0.6567 (m) REVERT: c 15 GLU cc_start: 0.7704 (mp0) cc_final: 0.7167 (mp0) REVERT: d 16 LYS cc_start: 0.3989 (tttt) cc_final: 0.1621 (mttt) REVERT: d 31 ARG cc_start: 0.5981 (tpm170) cc_final: 0.5265 (mtm180) REVERT: e 36 LEU cc_start: 0.5843 (mm) cc_final: 0.5519 (mt) REVERT: f 81 ARG cc_start: 0.7399 (mmm160) cc_final: 0.6860 (mmt180) REVERT: h 77 PHE cc_start: 0.5060 (m-80) cc_final: 0.4777 (m-80) REVERT: h 113 PHE cc_start: 0.1809 (m-80) cc_final: 0.0929 (m-80) REVERT: h 225 LYS cc_start: 0.5109 (tptp) cc_final: 0.4827 (tmmt) REVERT: h 234 ASP cc_start: 0.3509 (t0) cc_final: 0.2144 (m-30) REVERT: h 265 ILE cc_start: 0.5753 (tp) cc_final: 0.5531 (mp) REVERT: n 18 ARG cc_start: 0.3827 (ttm110) cc_final: 0.3072 (tpt170) REVERT: n 20 MET cc_start: 0.6834 (ppp) cc_final: 0.5942 (tpp) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.7681 time to fit residues: 710.9187 Evaluate side-chains 412 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 392 optimal weight: 0.0170 chunk 253 optimal weight: 0.0570 chunk 379 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 3.9990 chunk 432 optimal weight: 30.0000 chunk 314 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 499 optimal weight: 0.0770 overall best weight: 1.8298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS D 115 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 GLN X 91 ASN e 41 GLN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 84105 Z= 0.138 Angle : 0.559 12.057 122449 Z= 0.279 Chirality : 0.034 0.266 15194 Planarity : 0.004 0.062 8634 Dihedral : 23.272 178.997 34536 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 0.02 % Allowed : 0.83 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.41 (0.12), residues: 4821 helix: 0.57 (0.13), residues: 1484 sheet: -1.22 (0.18), residues: 757 loop : -1.80 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP h 43 HIS 0.005 0.001 HIS M 106 PHE 0.021 0.001 PHE D 97 TYR 0.049 0.001 TYR O 38 ARG 0.008 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 562 time to evaluate : 4.392 Fit side-chains REVERT: B 10 MET cc_start: 0.5683 (tpp) cc_final: 0.4608 (tpp) REVERT: B 120 ARG cc_start: 0.4954 (mmm-85) cc_final: 0.4534 (mmm160) REVERT: B 195 TRP cc_start: 0.5665 (p-90) cc_final: 0.5369 (p-90) REVERT: C 34 LYS cc_start: 0.4977 (mmtt) cc_final: 0.4513 (mmmt) REVERT: C 103 MET cc_start: 0.6412 (tmm) cc_final: 0.5980 (tmm) REVERT: C 175 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6052 (tp30) REVERT: D 65 LYS cc_start: 0.7174 (pttm) cc_final: 0.6634 (ptpt) REVERT: D 83 LEU cc_start: 0.7823 (mt) cc_final: 0.7222 (mt) REVERT: E 1 MET cc_start: 0.0886 (ptt) cc_final: 0.0008 (tpp) REVERT: E 41 VAL cc_start: 0.3308 (m) cc_final: 0.2983 (p) REVERT: E 127 MET cc_start: 0.4977 (mmp) cc_final: 0.4535 (mtm) REVERT: G 42 LYS cc_start: 0.4521 (mppt) cc_final: 0.3975 (tptm) REVERT: H 52 ILE cc_start: 0.6294 (pt) cc_final: 0.6058 (pt) REVERT: H 105 ASN cc_start: 0.7313 (t0) cc_final: 0.7022 (t0) REVERT: I 32 MET cc_start: 0.5537 (tpp) cc_final: 0.5270 (tpp) REVERT: I 127 ASP cc_start: 0.6631 (t0) cc_final: 0.6227 (t70) REVERT: I 131 GLU cc_start: 0.7321 (pp20) cc_final: 0.7026 (tm-30) REVERT: I 157 HIS cc_start: 0.6892 (m-70) cc_final: 0.6158 (m90) REVERT: J 27 TYR cc_start: 0.6887 (p90) cc_final: 0.6263 (p90) REVERT: J 109 TYR cc_start: 0.6116 (m-80) cc_final: 0.5879 (m-80) REVERT: J 174 CYS cc_start: 0.7179 (m) cc_final: 0.6961 (m) REVERT: J 205 ARG cc_start: 0.6940 (tpt90) cc_final: 0.6312 (ttm-80) REVERT: K 45 ARG cc_start: 0.5282 (ttp-170) cc_final: 0.5023 (tmm-80) REVERT: K 53 ILE cc_start: 0.7467 (mt) cc_final: 0.7263 (tt) REVERT: K 66 LYS cc_start: 0.6060 (mmtt) cc_final: 0.4614 (ttmm) REVERT: K 84 ILE cc_start: 0.7424 (mm) cc_final: 0.7046 (tt) REVERT: K 104 ASP cc_start: 0.6818 (m-30) cc_final: 0.6466 (t0) REVERT: K 148 ILE cc_start: 0.8833 (mm) cc_final: 0.8612 (mt) REVERT: K 175 ARG cc_start: 0.6276 (ptt180) cc_final: 0.5183 (ptm160) REVERT: L 1 MET cc_start: 0.3536 (tpt) cc_final: 0.2943 (tpp) REVERT: L 12 TYR cc_start: 0.4802 (m-80) cc_final: 0.4483 (m-80) REVERT: M 118 ARG cc_start: 0.5227 (mtm-85) cc_final: 0.4631 (ttm110) REVERT: M 152 LYS cc_start: 0.0922 (ptmt) cc_final: -0.0140 (pttm) REVERT: P 124 MET cc_start: 0.5664 (mmp) cc_final: 0.5363 (mmp) REVERT: P 128 ARG cc_start: 0.6333 (mmt180) cc_final: 0.5428 (tpp-160) REVERT: Q 25 LEU cc_start: 0.4274 (mt) cc_final: 0.3901 (tp) REVERT: Q 31 GLU cc_start: 0.6329 (mp0) cc_final: 0.5398 (pm20) REVERT: Q 37 TYR cc_start: 0.4295 (p90) cc_final: 0.4068 (p90) REVERT: Q 88 GLU cc_start: 0.4937 (tm-30) cc_final: 0.4735 (tm-30) REVERT: R 63 PHE cc_start: 0.5474 (m-80) cc_final: 0.5187 (m-80) REVERT: R 109 LYS cc_start: 0.6635 (pttt) cc_final: 0.6250 (mmmt) REVERT: S 21 TYR cc_start: 0.5923 (t80) cc_final: 0.5597 (t80) REVERT: S 108 LEU cc_start: 0.6595 (pp) cc_final: 0.6113 (mp) REVERT: T 24 ARG cc_start: 0.2408 (mtt180) cc_final: 0.2028 (mmt90) REVERT: T 28 PHE cc_start: 0.2918 (m-80) cc_final: 0.1107 (t80) REVERT: T 76 GLN cc_start: 0.6515 (mp10) cc_final: 0.5743 (tp-100) REVERT: U 75 MET cc_start: 0.8633 (mpp) cc_final: 0.7880 (mmp) REVERT: U 78 ILE cc_start: 0.6440 (pt) cc_final: 0.5248 (pt) REVERT: V 75 LYS cc_start: 0.5424 (mptt) cc_final: 0.4974 (mmtp) REVERT: V 77 TRP cc_start: 0.7058 (m100) cc_final: 0.6667 (m100) REVERT: W 15 ARG cc_start: 0.5139 (mtp180) cc_final: 0.4779 (mtm180) REVERT: W 61 ARG cc_start: 0.6520 (ttt180) cc_final: 0.6103 (ttp-170) REVERT: X 12 LYS cc_start: 0.7207 (tmmt) cc_final: 0.6422 (tppp) REVERT: X 40 VAL cc_start: 0.8122 (p) cc_final: 0.7814 (m) REVERT: X 88 LYS cc_start: 0.7038 (tptt) cc_final: 0.6423 (tptp) REVERT: Y 25 LYS cc_start: 0.5686 (ttmt) cc_final: 0.4898 (tttm) REVERT: Y 27 TYR cc_start: 0.6136 (t80) cc_final: 0.5930 (t80) REVERT: Z 44 LEU cc_start: 0.8116 (tp) cc_final: 0.7913 (pp) REVERT: Z 80 ASP cc_start: 0.8165 (p0) cc_final: 0.7813 (p0) REVERT: Z 114 MET cc_start: 0.7478 (ttp) cc_final: 0.6739 (tmm) REVERT: b 81 SER cc_start: 0.5598 (m) cc_final: 0.5042 (p) REVERT: b 88 SER cc_start: 0.6792 (p) cc_final: 0.6299 (m) REVERT: b 94 ASP cc_start: 0.6342 (m-30) cc_final: 0.5383 (t70) REVERT: c 15 GLU cc_start: 0.7636 (mp0) cc_final: 0.7156 (mp0) REVERT: c 72 ARG cc_start: 0.6439 (tpp80) cc_final: 0.5989 (tpp-160) REVERT: d 16 LYS cc_start: 0.3969 (tttt) cc_final: 0.1499 (mttt) REVERT: d 31 ARG cc_start: 0.5851 (tpm170) cc_final: 0.5259 (mtm180) REVERT: f 81 ARG cc_start: 0.7281 (mmm160) cc_final: 0.6488 (mmt180) REVERT: h 225 LYS cc_start: 0.5071 (tptp) cc_final: 0.4846 (tmmt) REVERT: h 234 ASP cc_start: 0.3593 (t0) cc_final: 0.2424 (m-30) REVERT: h 282 GLU cc_start: 0.6010 (tp30) cc_final: 0.5562 (tp30) REVERT: n 18 ARG cc_start: 0.3928 (ttm110) cc_final: 0.3136 (tpt170) REVERT: n 20 MET cc_start: 0.6842 (ppp) cc_final: 0.5881 (tpp) outliers start: 1 outliers final: 0 residues processed: 562 average time/residue: 0.7565 time to fit residues: 727.4273 Evaluate side-chains 424 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 4.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 577 optimal weight: 10.0000 chunk 608 optimal weight: 30.0000 chunk 555 optimal weight: 5.9990 chunk 591 optimal weight: 3.9990 chunk 356 optimal weight: 7.9990 chunk 257 optimal weight: 0.5980 chunk 464 optimal weight: 0.0070 chunk 181 optimal weight: 0.0270 chunk 534 optimal weight: 5.9990 chunk 559 optimal weight: 20.0000 chunk 589 optimal weight: 9.9990 overall best weight: 2.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 GLN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 120 HIS ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 84105 Z= 0.139 Angle : 0.553 10.481 122449 Z= 0.275 Chirality : 0.034 0.270 15194 Planarity : 0.004 0.064 8634 Dihedral : 23.207 178.712 34536 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.62 % Favored : 94.36 % Rotamer: Outliers : 0.02 % Allowed : 0.57 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.28 (0.12), residues: 4821 helix: 0.70 (0.13), residues: 1478 sheet: -1.06 (0.18), residues: 752 loop : -1.75 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP h 83 HIS 0.016 0.001 HIS h 191 PHE 0.027 0.001 PHE T 83 TYR 0.052 0.001 TYR O 38 ARG 0.008 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 531 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 MET cc_start: 0.5803 (tpp) cc_final: 0.4693 (tpp) REVERT: B 120 ARG cc_start: 0.5057 (mmm-85) cc_final: 0.4494 (mmm160) REVERT: B 195 TRP cc_start: 0.5727 (p-90) cc_final: 0.5451 (p-90) REVERT: C 34 LYS cc_start: 0.5003 (mmtt) cc_final: 0.4557 (mmmt) REVERT: C 103 MET cc_start: 0.6327 (tmm) cc_final: 0.5261 (tmm) REVERT: C 113 MET cc_start: 0.5644 (mtp) cc_final: 0.5365 (mtp) REVERT: C 175 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5805 (tp30) REVERT: D 65 LYS cc_start: 0.7190 (pttm) cc_final: 0.6689 (ptpt) REVERT: D 83 LEU cc_start: 0.7839 (mt) cc_final: 0.7208 (mt) REVERT: D 215 MET cc_start: 0.6205 (ttm) cc_final: 0.5964 (ttt) REVERT: E 1 MET cc_start: 0.1178 (ptt) cc_final: 0.0089 (tpp) REVERT: E 41 VAL cc_start: 0.3282 (m) cc_final: 0.2945 (p) REVERT: E 127 MET cc_start: 0.4951 (mmp) cc_final: 0.4398 (mtm) REVERT: F 16 LYS cc_start: 0.7539 (tttp) cc_final: 0.7294 (ttmm) REVERT: F 66 MET cc_start: 0.4506 (ttp) cc_final: 0.4239 (ttp) REVERT: F 181 CYS cc_start: 0.8412 (t) cc_final: 0.8196 (t) REVERT: G 42 LYS cc_start: 0.4695 (mppt) cc_final: 0.4135 (tptm) REVERT: G 82 ASN cc_start: 0.3367 (m-40) cc_final: 0.3147 (m-40) REVERT: H 52 ILE cc_start: 0.6248 (pt) cc_final: 0.6026 (pt) REVERT: H 105 ASN cc_start: 0.7362 (t0) cc_final: 0.7089 (t0) REVERT: I 32 MET cc_start: 0.5563 (tpp) cc_final: 0.5323 (tpp) REVERT: I 127 ASP cc_start: 0.6642 (t0) cc_final: 0.6218 (t70) REVERT: I 131 GLU cc_start: 0.7231 (pp20) cc_final: 0.6877 (tm-30) REVERT: I 157 HIS cc_start: 0.6870 (m-70) cc_final: 0.6223 (m90) REVERT: J 109 TYR cc_start: 0.6116 (m-80) cc_final: 0.5886 (m-80) REVERT: J 174 CYS cc_start: 0.7173 (m) cc_final: 0.6859 (m) REVERT: J 205 ARG cc_start: 0.6952 (tpt90) cc_final: 0.6308 (ttm-80) REVERT: K 35 TYR cc_start: 0.7062 (m-80) cc_final: 0.6718 (m-80) REVERT: K 45 ARG cc_start: 0.5311 (ttp-170) cc_final: 0.5068 (tmm-80) REVERT: K 84 ILE cc_start: 0.7383 (mm) cc_final: 0.7019 (tt) REVERT: K 104 ASP cc_start: 0.6850 (m-30) cc_final: 0.6386 (t0) REVERT: K 148 ILE cc_start: 0.8860 (mm) cc_final: 0.8592 (mt) REVERT: K 175 ARG cc_start: 0.6282 (ptt180) cc_final: 0.5186 (ptm160) REVERT: L 1 MET cc_start: 0.3536 (tpt) cc_final: 0.2984 (tpp) REVERT: L 12 TYR cc_start: 0.4855 (m-80) cc_final: 0.4643 (m-80) REVERT: M 118 ARG cc_start: 0.5071 (mtm-85) cc_final: 0.4590 (ttm110) REVERT: M 152 LYS cc_start: 0.0918 (ptmt) cc_final: -0.0151 (pttm) REVERT: P 128 ARG cc_start: 0.6358 (mmt180) cc_final: 0.5438 (tpp-160) REVERT: Q 25 LEU cc_start: 0.4783 (mt) cc_final: 0.4387 (tp) REVERT: Q 31 GLU cc_start: 0.6235 (mp0) cc_final: 0.5299 (pm20) REVERT: Q 89 MET cc_start: 0.3302 (mtt) cc_final: 0.2913 (mtm) REVERT: R 63 PHE cc_start: 0.5585 (m-80) cc_final: 0.5303 (m-80) REVERT: R 69 ARG cc_start: 0.6384 (mtp85) cc_final: 0.5699 (tmm160) REVERT: R 109 LYS cc_start: 0.6590 (pttt) cc_final: 0.6289 (mmmt) REVERT: S 21 TYR cc_start: 0.5934 (t80) cc_final: 0.5617 (t80) REVERT: S 108 LEU cc_start: 0.6656 (pp) cc_final: 0.6145 (mp) REVERT: S 121 GLN cc_start: 0.6844 (pm20) cc_final: 0.6516 (mp10) REVERT: T 24 ARG cc_start: 0.2193 (mtt180) cc_final: 0.1972 (mmt90) REVERT: T 76 GLN cc_start: 0.6475 (mp10) cc_final: 0.5698 (tp-100) REVERT: U 75 MET cc_start: 0.8658 (mpp) cc_final: 0.7889 (mmp) REVERT: U 78 ILE cc_start: 0.6413 (pt) cc_final: 0.5203 (pt) REVERT: V 75 LYS cc_start: 0.5542 (mptt) cc_final: 0.4956 (mmtp) REVERT: V 77 TRP cc_start: 0.7031 (m100) cc_final: 0.6597 (m100) REVERT: V 78 ASP cc_start: 0.6425 (p0) cc_final: 0.6202 (p0) REVERT: W 15 ARG cc_start: 0.5155 (mtp180) cc_final: 0.4786 (mtm180) REVERT: X 88 LYS cc_start: 0.7040 (tptt) cc_final: 0.6369 (tptp) REVERT: Y 25 LYS cc_start: 0.5571 (ttmt) cc_final: 0.4782 (tttm) REVERT: Y 27 TYR cc_start: 0.6188 (t80) cc_final: 0.5922 (t80) REVERT: Z 80 ASP cc_start: 0.8188 (p0) cc_final: 0.7838 (p0) REVERT: Z 114 MET cc_start: 0.7483 (ttp) cc_final: 0.6923 (tmm) REVERT: b 88 SER cc_start: 0.6793 (p) cc_final: 0.6265 (m) REVERT: b 94 ASP cc_start: 0.6323 (m-30) cc_final: 0.5406 (t70) REVERT: d 16 LYS cc_start: 0.3965 (tttt) cc_final: 0.1525 (mttt) REVERT: d 31 ARG cc_start: 0.5920 (tpm170) cc_final: 0.5306 (mtm180) REVERT: h 234 ASP cc_start: 0.3383 (t0) cc_final: 0.2353 (m-30) REVERT: n 1 MET cc_start: 0.6424 (tpt) cc_final: 0.5461 (tpp) REVERT: n 18 ARG cc_start: 0.3940 (ttm110) cc_final: 0.3219 (tpt170) REVERT: n 20 MET cc_start: 0.6870 (ppp) cc_final: 0.5816 (tpp) outliers start: 1 outliers final: 0 residues processed: 532 average time/residue: 0.7473 time to fit residues: 680.6548 Evaluate side-chains 413 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 4.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 388 optimal weight: 0.6980 chunk 625 optimal weight: 9.9990 chunk 382 optimal weight: 0.0000 chunk 296 optimal weight: 5.9990 chunk 435 optimal weight: 10.0000 chunk 656 optimal weight: 30.0000 chunk 604 optimal weight: 2.9990 chunk 522 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 0.9980 chunk 320 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 84105 Z= 0.127 Angle : 0.539 11.518 122449 Z= 0.268 Chirality : 0.033 0.310 15194 Planarity : 0.004 0.108 8634 Dihedral : 23.136 178.900 34536 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.35 % Favored : 94.63 % Rotamer: Outliers : 0.02 % Allowed : 0.31 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.21 (0.12), residues: 4821 helix: 0.73 (0.13), residues: 1473 sheet: -1.05 (0.19), residues: 748 loop : -1.67 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP h 83 HIS 0.014 0.001 HIS h 191 PHE 0.021 0.001 PHE T 83 TYR 0.020 0.001 TYR h 246 ARG 0.013 0.000 ARG f 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 5.640 Fit side-chains REVERT: B 10 MET cc_start: 0.5790 (tpp) cc_final: 0.4703 (tpp) REVERT: B 120 ARG cc_start: 0.5044 (mmm-85) cc_final: 0.4516 (mmm160) REVERT: B 195 TRP cc_start: 0.5714 (p-90) cc_final: 0.5473 (p-90) REVERT: C 34 LYS cc_start: 0.4850 (mmtt) cc_final: 0.4457 (mmmt) REVERT: C 103 MET cc_start: 0.6308 (tmm) cc_final: 0.5330 (tmm) REVERT: C 113 MET cc_start: 0.5576 (mtp) cc_final: 0.5312 (mtp) REVERT: C 175 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5858 (tp30) REVERT: D 65 LYS cc_start: 0.7158 (pttm) cc_final: 0.6681 (ptpt) REVERT: D 83 LEU cc_start: 0.7772 (mt) cc_final: 0.7161 (mt) REVERT: D 194 ARG cc_start: 0.7169 (ttt180) cc_final: 0.6843 (ttt-90) REVERT: D 215 MET cc_start: 0.6173 (ttm) cc_final: 0.5914 (ttt) REVERT: E 1 MET cc_start: 0.1112 (ptt) cc_final: -0.0004 (tpt) REVERT: E 41 VAL cc_start: 0.3387 (m) cc_final: 0.3024 (p) REVERT: E 127 MET cc_start: 0.4976 (mmp) cc_final: 0.4478 (mtm) REVERT: F 40 GLU cc_start: 0.6462 (pm20) cc_final: 0.6229 (pm20) REVERT: G 42 LYS cc_start: 0.4369 (mppt) cc_final: 0.3856 (tptm) REVERT: G 82 ASN cc_start: 0.3443 (m-40) cc_final: 0.3171 (m-40) REVERT: H 105 ASN cc_start: 0.7332 (t0) cc_final: 0.7093 (t0) REVERT: I 32 MET cc_start: 0.5472 (tpp) cc_final: 0.5242 (tpp) REVERT: I 73 GLN cc_start: 0.6817 (mp10) cc_final: 0.6611 (mp10) REVERT: I 127 ASP cc_start: 0.6715 (t0) cc_final: 0.6287 (t70) REVERT: I 131 GLU cc_start: 0.7234 (pp20) cc_final: 0.6881 (tm-30) REVERT: I 157 HIS cc_start: 0.6899 (m-70) cc_final: 0.6287 (m90) REVERT: J 27 TYR cc_start: 0.6750 (p90) cc_final: 0.6160 (p90) REVERT: J 109 TYR cc_start: 0.6314 (m-80) cc_final: 0.6089 (m-80) REVERT: J 174 CYS cc_start: 0.7186 (m) cc_final: 0.6911 (m) REVERT: J 205 ARG cc_start: 0.6933 (tpt90) cc_final: 0.6305 (ttm-80) REVERT: K 35 TYR cc_start: 0.7020 (m-80) cc_final: 0.6657 (m-80) REVERT: K 45 ARG cc_start: 0.5331 (ttp-170) cc_final: 0.5075 (tmm-80) REVERT: K 84 ILE cc_start: 0.7382 (mm) cc_final: 0.7002 (tt) REVERT: K 104 ASP cc_start: 0.6806 (m-30) cc_final: 0.6427 (t0) REVERT: K 148 ILE cc_start: 0.8846 (mm) cc_final: 0.8628 (mt) REVERT: K 175 ARG cc_start: 0.6282 (ptt180) cc_final: 0.5383 (ptm160) REVERT: L 1 MET cc_start: 0.3608 (tpt) cc_final: 0.3045 (tpp) REVERT: M 118 ARG cc_start: 0.5067 (mtm-85) cc_final: 0.4618 (ttm110) REVERT: M 152 LYS cc_start: 0.0977 (ptmt) cc_final: -0.0093 (pttm) REVERT: P 124 MET cc_start: 0.5689 (mmp) cc_final: 0.5421 (mmp) REVERT: P 128 ARG cc_start: 0.6405 (mmt180) cc_final: 0.5529 (tpp-160) REVERT: Q 25 LEU cc_start: 0.4812 (mt) cc_final: 0.4331 (tp) REVERT: Q 31 GLU cc_start: 0.6221 (mp0) cc_final: 0.5041 (pm20) REVERT: R 63 PHE cc_start: 0.5441 (m-80) cc_final: 0.5160 (m-80) REVERT: R 69 ARG cc_start: 0.6300 (mtp85) cc_final: 0.5666 (tmm160) REVERT: R 96 TYR cc_start: 0.3341 (m-80) cc_final: 0.3106 (m-10) REVERT: R 100 VAL cc_start: 0.5380 (m) cc_final: 0.5074 (p) REVERT: R 109 LYS cc_start: 0.6699 (pttt) cc_final: 0.6418 (mmmt) REVERT: S 21 TYR cc_start: 0.5867 (t80) cc_final: 0.5554 (t80) REVERT: S 108 LEU cc_start: 0.6423 (pp) cc_final: 0.5893 (mt) REVERT: S 121 GLN cc_start: 0.6855 (pm20) cc_final: 0.6544 (mp10) REVERT: T 24 ARG cc_start: 0.2733 (mtt180) cc_final: 0.2524 (mmt90) REVERT: T 76 GLN cc_start: 0.6462 (mp10) cc_final: 0.5671 (tp-100) REVERT: U 75 MET cc_start: 0.8464 (mpp) cc_final: 0.7457 (mmp) REVERT: U 78 ILE cc_start: 0.6439 (pt) cc_final: 0.4914 (pt) REVERT: V 75 LYS cc_start: 0.5517 (mptt) cc_final: 0.4925 (mmtp) REVERT: V 77 TRP cc_start: 0.6965 (m100) cc_final: 0.6544 (m100) REVERT: W 15 ARG cc_start: 0.5125 (mtp180) cc_final: 0.4703 (mtm180) REVERT: W 61 ARG cc_start: 0.6475 (ttt180) cc_final: 0.5816 (ttp-170) REVERT: Y 25 LYS cc_start: 0.5484 (ttmt) cc_final: 0.4748 (tttm) REVERT: Z 74 MET cc_start: 0.5896 (mtm) cc_final: 0.5618 (mtm) REVERT: Z 80 ASP cc_start: 0.8163 (p0) cc_final: 0.7706 (p0) REVERT: Z 114 MET cc_start: 0.7610 (ttp) cc_final: 0.7025 (tmm) REVERT: b 88 SER cc_start: 0.6764 (p) cc_final: 0.6291 (m) REVERT: b 94 ASP cc_start: 0.6269 (m-30) cc_final: 0.5347 (t70) REVERT: d 16 LYS cc_start: 0.3864 (tttt) cc_final: 0.1411 (mttt) REVERT: d 31 ARG cc_start: 0.5859 (tpm170) cc_final: 0.5320 (mtm180) REVERT: f 81 ARG cc_start: 0.7257 (mmm160) cc_final: 0.6500 (mmt180) REVERT: h 234 ASP cc_start: 0.3521 (t0) cc_final: 0.2602 (m-30) REVERT: h 282 GLU cc_start: 0.6065 (tp30) cc_final: 0.5602 (tp30) REVERT: n 18 ARG cc_start: 0.3987 (ttm110) cc_final: 0.3226 (tpt170) REVERT: n 20 MET cc_start: 0.6902 (ppp) cc_final: 0.5816 (tpp) outliers start: 1 outliers final: 1 residues processed: 536 average time/residue: 0.7612 time to fit residues: 702.4806 Evaluate side-chains 418 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 415 optimal weight: 6.9990 chunk 556 optimal weight: 9.9990 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 40.0000 chunk 523 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 537 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 ASN ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN I 162 GLN I 165 ASN ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS T 17 ASN U 12 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.069021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057611 restraints weight = 580891.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.057745 restraints weight = 394624.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057795 restraints weight = 319149.278| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 84105 Z= 0.311 Angle : 0.766 16.559 122449 Z= 0.378 Chirality : 0.042 0.353 15194 Planarity : 0.006 0.102 8634 Dihedral : 23.555 177.356 34536 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.59 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.78 (0.12), residues: 4821 helix: 0.14 (0.13), residues: 1480 sheet: -1.44 (0.18), residues: 767 loop : -1.94 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP U 33 HIS 0.013 0.002 HIS h 191 PHE 0.027 0.003 PHE Z 60 TYR 0.047 0.003 TYR O 38 ARG 0.020 0.001 ARG Q 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13580.32 seconds wall clock time: 239 minutes 18.53 seconds (14358.53 seconds total)