Starting phenix.real_space_refine on Mon Sep 30 06:06:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/09_2024/7syk_25531.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/09_2024/7syk_25531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/09_2024/7syk_25531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/09_2024/7syk_25531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/09_2024/7syk_25531.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syk_25531/09_2024/7syk_25531.cif" } resolution = 4.2 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 77 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': 143, 'rna2p_pyr': 111, 'rna3p_pur': 754, 'rna3p_pyr': 689} Link IDs: {'rna2p': 253, 'rna3p': 1443} 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': 11, 'rna2p_pyr': 14, 'rna3p_pur': 73, 'rna3p_pyr': 64} Link IDs: {'rna2p': 24, 'rna3p': 137} 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 92.426 129.436 137.590 1.00 60.60 S ATOM 69352 SG CYS b 26 95.952 129.735 138.598 1.00 59.74 S ATOM 69735 SG CYS b 74 95.016 126.338 139.031 1.00 53.29 S ATOM 69754 SG CYS b 77 94.927 127.998 140.396 1.00 51.40 S ATOM 72396 SG CYS g 121 149.395 98.945 244.281 1.00244.74 S ATOM 72432 SG CYS g 126 148.469 96.439 242.787 1.00249.60 S ATOM 72550 SG CYS g 141 149.506 99.698 242.311 1.00240.65 S ATOM 72569 SG CYS g 144 145.927 99.998 242.732 1.00241.16 S Time building chain proxies: 31.58, per 1000 atoms: 0.40 Number of scatterers: 78761 At special positions: 0 Unit cell: (234.65, 193.8, 261.25, 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: 13.55 Conformation dependent library (CDL) restraints added in 4.2 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 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " 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: 135 helices and 58 sheets defined 32.7% alpha, 16.2% beta 483 base pairs and 970 stacking pairs defined. Time for finding SS restraints: 24.04 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.820A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 36 removed outlier: 3.990A pdb=" N GLU B 35 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN B 36 " --> pdb=" O GLN B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 32 through 36' Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 50 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 85 through 95 Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.675A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.803A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 removed outlier: 4.214A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 4.220A pdb=" N ASN C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 Processing helix chain 'C' and resid 224 through 232 removed outlier: 4.157A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 4.027A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.623A 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 216 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.581A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS D 257 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 removed outlier: 5.831A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.757A pdb=" N ALA E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 44 through 51 Processing helix chain 'F' and resid 59 through 67 Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 67 through 74 Processing helix chain 'G' and resid 85 through 105 removed outlier: 4.145A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.967A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 183 removed outlier: 4.063A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA G 181 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 201 Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.669A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 34 removed outlier: 4.280A pdb=" N SER I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 73 Processing helix chain 'I' and resid 78 through 87 Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.132A 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 93 removed outlier: 3.858A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR J 93 " --> pdb=" O GLU J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 88 through 93' 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: 3.703A 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: 3.561A pdb=" N GLU J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.417A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 93 through 97 removed outlier: 3.850A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 108 removed outlier: 3.835A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG K 108 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.945A 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 171 through 186 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.618A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 9 " --> pdb=" O LYS L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.975A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 52 removed outlier: 3.903A pdb=" N ILE M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 28 Processing helix chain 'N' and resid 34 through 45 Processing helix chain 'N' and resid 60 through 70 removed outlier: 4.389A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 90 removed outlier: 3.646A pdb=" N GLU N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 43 removed outlier: 3.525A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.704A 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 104 Processing helix chain 'O' and resid 109 through 132 removed outlier: 3.706A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 removed outlier: 3.694A pdb=" N ALA P 74 " --> pdb=" O SER P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 122 removed outlier: 3.635A pdb=" N SER P 122 " --> pdb=" O ALA P 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 28 removed outlier: 3.697A pdb=" N MET Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.955A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 46 removed outlier: 3.595A pdb=" N ARG Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG Q 44 " --> pdb=" O ARG Q 40 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 63 Proline residue: R 54 - end of helix removed outlier: 7.197A pdb=" N LYS R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N GLU R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG R 62 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE R 63 " --> pdb=" O GLY R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 100 removed outlier: 3.871A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 4.266A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 removed outlier: 3.611A pdb=" N LEU R 120 " --> pdb=" O ARG R 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 117 through 120' Processing helix chain 'S' and resid 6 through 18 removed outlier: 4.037A pdb=" N LYS S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL S 15 " --> pdb=" O LYS S 11 " (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 79 through 84 removed outlier: 3.971A pdb=" N ASP S 82 " --> pdb=" O GLU S 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN S 83 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR S 84 " --> pdb=" O ARG S 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 79 through 84' Processing helix chain 'S' and resid 99 through 107 Processing helix chain 'T' and resid 29 through 33 removed outlier: 3.588A pdb=" N ALA T 32 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.508A pdb=" N ALA T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL T 44 " --> pdb=" O TYR T 40 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG T 46 " --> pdb=" O HIS T 42 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS T 47 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 37 through 48' Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 99 through 117 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 10 through 26 removed outlier: 4.027A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 35 removed outlier: 4.017A pdb=" N VAL U 34 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 31 through 35' Processing helix chain 'U' and resid 51 through 67 removed outlier: 4.007A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 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 104 Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.977A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 77 removed outlier: 3.646A pdb=" N SER W 68 " --> pdb=" O GLU W 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 Processing helix chain 'X' and resid 85 through 93 removed outlier: 3.530A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 120 removed outlier: 3.895A 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 25 through 31 Processing helix chain 'Y' and resid 32 through 39 removed outlier: 4.015A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 136 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 4.013A 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 94 removed outlier: 3.604A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.705A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL Z 117 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 removed outlier: 4.072A pdb=" N ASN Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 62 Processing helix chain 'a' and resid 69 through 77 Processing helix chain 'a' and resid 80 through 95 removed outlier: 3.746A pdb=" N ALA a 84 " --> pdb=" O ARG a 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 Processing helix chain 'e' and resid 2 through 6 Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.686A pdb=" N LEU e 36 " --> pdb=" O LYS e 33 " (cutoff:3.500A) 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 24 removed outlier: 3.559A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 removed outlier: 4.010A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.641A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.542A pdb=" N TYR C 31 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 13.769A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.542A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 215 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 137 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 70 removed outlier: 5.444A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 13.769A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.542A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 215 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 140 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 210 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE C 142 " --> pdb=" O HIS C 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.120A pdb=" N LYS D 103 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 131 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.120A pdb=" N LYS D 103 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 131 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.604A pdb=" N VAL D 184 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 225 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 36 through 39 removed outlier: 3.686A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 38 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E 49 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 87 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.685A pdb=" N PHE E 152 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS E 134 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 188 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.685A pdb=" N PHE E 152 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS E 134 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 175 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE E 184 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 3.554A 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: 4.592A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.750A pdb=" N GLU F 97 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.288A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.631A pdb=" N VAL F 140 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS F 122 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 162 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 217 through 221 removed outlier: 3.659A pdb=" N VAL F 207 " --> pdb=" O GLU F 199 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN F 197 " --> pdb=" O HIS F 209 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS F 211 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE F 195 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AB9, first strand: chain 'G' and resid 123 through 124 removed outlier: 3.813A pdb=" N ASP G 124 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG d 44 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N CYS d 27 " --> pdb=" O GLY d 19 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY d 19 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.833A pdb=" N CYS H 12 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LYS H 2 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU H 111 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN H 4 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE H 113 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER H 6 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N LYS H 115 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.666A pdb=" N VAL H 73 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL H 97 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 47 through 52 removed outlier: 3.902A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL I 93 " --> pdb=" O ILE I 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 185 through 188 removed outlier: 4.139A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AC6, first strand: chain 'J' and resid 42 through 44 removed outlier: 6.893A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.598A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE J 175 " --> pdb=" O CYS J 100 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AC9, first strand: chain 'L' and resid 62 through 63 Processing sheet with id=AD1, first strand: chain 'M' and resid 72 through 73 removed outlier: 7.584A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU M 143 " --> pdb=" O THR M 127 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG M 101 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 31 through 33 removed outlier: 3.875A pdb=" N VAL N 109 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL N 79 " --> pdb=" O CYS N 50 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU N 52 " --> pdb=" O VAL N 79 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 52 through 56 removed outlier: 7.371A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU P 93 " --> pdb=" O ILE P 126 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG P 128 " --> pdb=" O LEU P 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 75 through 77 removed outlier: 4.150A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN Q 98 " --> pdb=" O THR Q 101 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR Q 101 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 11 through 13 removed outlier: 3.600A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS R 33 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL R 70 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 97 through 98 Processing sheet with id=AD7, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.762A pdb=" N ILE T 20 " --> pdb=" O LEU T 13 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL T 15 " --> pdb=" O THR T 18 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 81 through 83 removed outlier: 3.826A pdb=" N HIS U 91 " --> pdb=" O GLN U 83 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE1, first strand: chain 'V' and resid 59 through 66 removed outlier: 3.580A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP V 78 " --> pdb=" O THR V 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS V 85 " --> pdb=" O SER V 26 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR V 25 " --> pdb=" O GLU V 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 59 through 66 removed outlier: 3.580A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP V 78 " --> pdb=" O THR V 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS V 85 " --> pdb=" O SER V 26 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 32 through 39 removed outlier: 3.589A pdb=" N ILE W 32 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE W 55 " --> pdb=" O ILE W 32 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU W 38 " --> pdb=" O GLN W 49 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 71 through 74 removed outlier: 5.679A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY X 127 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 80 through 82 removed outlier: 7.618A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU Y 52 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS Y 124 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 57 through 58 Processing sheet with id=AE7, first strand: chain 'Z' and resid 6 through 15 removed outlier: 5.966A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE Z 72 " --> pdb=" O GLY Z 59 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY Z 59 " --> pdb=" O PHE Z 72 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET Z 74 " --> pdb=" O VAL Z 57 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL Z 57 " --> pdb=" O MET Z 74 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR Z 76 " --> pdb=" O ILE Z 55 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE Z 55 " --> pdb=" O TYR Z 76 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'a' and resid 67 through 68 removed outlier: 3.902A pdb=" N TYR a 109 " --> pdb=" O ILE a 68 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF1, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.517A pdb=" N ILE b 36 " --> pdb=" O TYR b 73 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 44 through 47 removed outlier: 3.822A pdb=" N THR c 44 " --> pdb=" O VAL c 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 54 through 55 removed outlier: 6.921A pdb=" N VAL c 54 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU c 63 " --> pdb=" O VAL c 54 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 30 through 31 Processing sheet with id=AF5, first strand: chain 'g' and resid 133 through 134 removed outlier: 3.679A pdb=" N ALA g 133 " --> pdb=" O TYR g 140 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'h' and resid 5 through 10 removed outlier: 3.740A pdb=" N ARG h 8 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL h 309 " --> pdb=" O ARG h 8 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR h 10 " --> pdb=" O VAL h 307 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL h 307 " --> pdb=" O THR h 10 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 21 through 22 removed outlier: 3.689A pdb=" N LEU h 32 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN h 56 " --> pdb=" O MET h 42 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 66 through 71 removed outlier: 4.126A pdb=" N SER h 80 " --> pdb=" O ARG h 88 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 110 through 113 removed outlier: 3.519A pdb=" N SER h 122 " --> pdb=" O LYS h 130 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 151 through 155 Processing sheet with id=AG2, first strand: chain 'h' and resid 174 through 178 removed outlier: 5.375A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.553A pdb=" N THR h 199 " --> pdb=" O ALA h 208 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.251A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA h 250 " --> pdb=" O LYS h 257 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS h 257 " --> pdb=" O ALA h 250 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) 1360 hydrogen bonds defined for protein. 3897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1215 hydrogen bonds 2040 hydrogen bond angles 0 basepair planarities 483 basepair parallelities 970 stacking parallelities Total time for adding SS restraints: 59.29 Time building geometry restraints manager: 16.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14909 1.33 - 1.46: 30395 1.46 - 1.58: 34823 1.58 - 1.70: 3704 1.70 - 1.83: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" CA THR R 18 " pdb=" C THR R 18 " ideal model delta sigma weight residual 1.523 1.582 -0.059 1.34e-02 5.57e+03 1.91e+01 bond pdb=" C ILE C 189 " pdb=" N PRO C 190 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.80e+00 bond pdb=" O5' G z 267 " pdb=" C5' G z 267 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.64e+00 bond pdb=" O3' U 21114 " pdb=" P U 21115 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.62e+00 bond pdb=" P G z 266 " pdb=" OP2 G z 266 " ideal model delta sigma weight residual 1.485 1.528 -0.043 2.00e-02 2.50e+03 4.61e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 121425 3.64 - 7.29: 899 7.29 - 10.93: 112 10.93 - 14.57: 10 14.57 - 18.21: 3 Bond angle restraints: 122449 Sorted by residual: angle pdb=" C LEU O 45 " pdb=" N THR O 46 " pdb=" CA THR O 46 " ideal model delta sigma weight residual 120.49 136.99 -16.50 1.42e+00 4.96e-01 1.35e+02 angle pdb=" N ILE G 33 " pdb=" CA ILE G 33 " pdb=" C ILE G 33 " ideal model delta sigma weight residual 112.29 104.93 7.36 9.40e-01 1.13e+00 6.12e+01 angle pdb=" C GLY D 175 " pdb=" N LYS D 176 " pdb=" CA LYS D 176 " ideal model delta sigma weight residual 120.49 130.26 -9.77 1.42e+00 4.96e-01 4.73e+01 angle pdb=" CA LYS T 8 " pdb=" CB LYS T 8 " pdb=" CG LYS T 8 " ideal model delta sigma weight residual 114.10 127.07 -12.97 2.00e+00 2.50e-01 4.21e+01 angle pdb=" CA ARG L 65 " pdb=" CB ARG L 65 " pdb=" CG ARG L 65 " ideal model delta sigma weight residual 114.10 126.51 -12.41 2.00e+00 2.50e-01 3.85e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 48464 35.95 - 71.90: 4639 71.90 - 107.84: 575 107.84 - 143.79: 9 143.79 - 179.74: 27 Dihedral angle restraints: 53714 sinusoidal: 39658 harmonic: 14056 Sorted by residual: dihedral pdb=" C4' G 21204 " pdb=" C3' G 21204 " pdb=" C2' G 21204 " pdb=" C1' G 21204 " ideal model delta sinusoidal sigma weight residual -35.00 30.63 -65.63 1 8.00e+00 1.56e-02 8.81e+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 -160.00 19.74 -179.74 1 1.50e+01 4.44e-03 8.53e+01 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 5.40 -165.40 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 53711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 14652 0.106 - 0.213: 506 0.213 - 0.319: 31 0.319 - 0.425: 3 0.425 - 0.532: 2 Chirality restraints: 15194 Sorted by residual: chirality pdb=" CB ILE F 45 " pdb=" CA ILE F 45 " pdb=" CG1 ILE F 45 " pdb=" CG2 ILE F 45 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CB ILE I 144 " pdb=" CA ILE I 144 " pdb=" CG1 ILE I 144 " pdb=" CG2 ILE I 144 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CB VAL W 9 " pdb=" CA VAL W 9 " pdb=" CG1 VAL W 9 " pdb=" CG2 VAL W 9 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 64 " 0.058 2.00e-02 2.50e+03 4.79e-02 5.73e+01 pdb=" CG TRP L 64 " -0.127 2.00e-02 2.50e+03 pdb=" CD1 TRP L 64 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP L 64 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP L 64 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP L 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP L 64 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 64 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 64 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP L 64 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21753 " 0.041 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" N1 C 21753 " -0.048 2.00e-02 2.50e+03 pdb=" C2 C 21753 " 0.043 2.00e-02 2.50e+03 pdb=" O2 C 21753 " -0.035 2.00e-02 2.50e+03 pdb=" N3 C 21753 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C 21753 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C 21753 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C 21753 " -0.008 2.00e-02 2.50e+03 pdb=" C6 C 21753 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 962 " 0.040 2.00e-02 2.50e+03 1.93e-02 1.03e+01 pdb=" N9 A 2 962 " -0.049 2.00e-02 2.50e+03 pdb=" C8 A 2 962 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A 2 962 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A 2 962 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A 2 962 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A 2 962 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A 2 962 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 2 962 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A 2 962 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A 2 962 " -0.007 2.00e-02 2.50e+03 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 16090 2.78 - 3.31: 64639 3.31 - 3.84: 149668 3.84 - 4.37: 171295 4.37 - 4.90: 251413 Nonbonded interactions: 653105 Sorted by model distance: nonbonded pdb=" O PHE h 65 " pdb=" OG SER h 82 " model vdw 2.255 3.040 nonbonded pdb=" O LEU C 62 " pdb=" OG1 THR C 88 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR P 45 " pdb=" O GLU P 51 " model vdw 2.269 3.040 nonbonded pdb=" O2' C 21374 " pdb=" O2 C 21464 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR D 169 " pdb=" O GLY D 175 " model vdw 2.274 3.040 ... (remaining 653100 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: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 2.440 Check model and map are aligned: 0.450 Set scattering table: 0.560 Process input model: 182.040 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.230 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:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 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 0.076 84105 Z= 0.215 Angle : 0.831 18.213 122449 Z= 0.411 Chirality : 0.043 0.532 15194 Planarity : 0.006 0.076 8634 Dihedral : 22.202 179.739 44648 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.93 % Favored : 94.05 % Rotamer: Outliers : 0.02 % Allowed : 0.40 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.72 (0.11), residues: 4821 helix: -1.71 (0.11), residues: 1465 sheet: -1.13 (0.20), residues: 680 loop : -2.07 (0.11), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.127 0.002 TRP L 64 HIS 0.010 0.001 HIS K 134 PHE 0.029 0.002 PHE X 50 TYR 0.040 0.002 TYR D 82 ARG 0.013 0.001 ARG Y 14 *********************** 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 605 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 604 time to evaluate : 4.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7982 (mmtt) REVERT: C 169 MET cc_start: 0.7666 (mtm) cc_final: 0.7271 (mtp) REVERT: C 229 MET cc_start: 0.7000 (tmm) cc_final: 0.6699 (tmm) REVERT: C 230 GLU cc_start: 0.6421 (pt0) cc_final: 0.6182 (pt0) REVERT: E 210 ILE cc_start: 0.5892 (tt) cc_final: 0.5357 (mm) REVERT: K 59 GLU cc_start: 0.6928 (tp30) cc_final: 0.6632 (tp30) REVERT: L 2 LEU cc_start: 0.5553 (mp) cc_final: 0.4977 (pt) REVERT: L 15 LEU cc_start: 0.8316 (mt) cc_final: 0.7703 (mt) REVERT: M 37 TYR cc_start: 0.7271 (p90) cc_final: 0.7063 (p90) REVERT: Q 21 ASP cc_start: 0.5697 (m-30) cc_final: 0.5015 (m-30) REVERT: Q 28 MET cc_start: 0.4972 (tpt) cc_final: 0.4456 (tpp) REVERT: R 86 GLN cc_start: 0.5972 (tm-30) cc_final: 0.5628 (tp40) REVERT: S 18 GLU cc_start: 0.6331 (mp0) cc_final: 0.6068 (mp0) REVERT: T 104 ASP cc_start: 0.6944 (t0) cc_final: 0.6496 (m-30) REVERT: U 44 GLU cc_start: 0.7248 (pm20) cc_final: 0.6711 (tt0) REVERT: U 112 MET cc_start: 0.7277 (tpp) cc_final: 0.6882 (tpt) REVERT: V 25 THR cc_start: 0.4580 (t) cc_final: 0.4351 (t) REVERT: W 28 ASP cc_start: 0.6469 (t0) cc_final: 0.6074 (t70) REVERT: Y 14 ARG cc_start: 0.5806 (mmp80) cc_final: 0.5195 (tpp80) REVERT: Y 27 TYR cc_start: 0.7257 (t80) cc_final: 0.6456 (t80) REVERT: c 75 GLU cc_start: 0.3484 (pm20) cc_final: 0.3184 (pm20) REVERT: d 34 PHE cc_start: 0.2884 (m-10) cc_final: 0.2646 (m-80) REVERT: e 13 LYS cc_start: 0.7541 (mtmt) cc_final: 0.7114 (mttp) REVERT: h 184 LEU cc_start: 0.3045 (pp) cc_final: 0.2556 (pt) REVERT: h 185 LYS cc_start: 0.4784 (pptt) cc_final: 0.4544 (pptt) outliers start: 1 outliers final: 0 residues processed: 605 average time/residue: 0.7451 time to fit residues: 778.3397 Evaluate side-chains 422 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 4.412 ------------------------------------------------------------------------------- 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: 8.9990 chunk 499 optimal weight: 4.9990 chunk 277 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 336 optimal weight: 8.9990 chunk 266 optimal weight: 7.9990 chunk 516 optimal weight: 30.0000 chunk 199 optimal weight: 0.6980 chunk 314 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 598 optimal weight: 4.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 111 GLN B 132 GLN C 163 GLN D 113 GLN G 79 HIS G 95 HIS H 13 GLN H 65 GLN J 7 ASN O 105 ASN S 31 ASN V 85 HIS X 24 GLN X 44 HIS a 103 HIS d 29 GLN d 45 ASN g 135 HIS ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 84105 Z= 0.232 Angle : 0.644 9.711 122449 Z= 0.328 Chirality : 0.038 0.317 15194 Planarity : 0.005 0.064 8634 Dihedral : 23.349 179.481 34536 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.18 % Favored : 93.80 % Rotamer: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % 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: -1.91 (0.11), residues: 4821 helix: -0.29 (0.13), residues: 1496 sheet: -1.16 (0.19), residues: 728 loop : -1.92 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP L 64 HIS 0.007 0.001 HIS P 94 PHE 0.017 0.002 PHE D 236 TYR 0.038 0.002 TYR O 38 ARG 0.009 0.001 ARG L 65 *********************** 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 508 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 505 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 169 MET cc_start: 0.7796 (mtm) cc_final: 0.7402 (mtp) REVERT: C 229 MET cc_start: 0.6781 (tmm) cc_final: 0.6502 (tmm) REVERT: D 73 MET cc_start: 0.6117 (tmm) cc_final: 0.5886 (tmm) REVERT: D 146 GLU cc_start: 0.7571 (pm20) cc_final: 0.7328 (pp20) REVERT: G 78 MET cc_start: 0.7138 (tpp) cc_final: 0.6753 (tpt) REVERT: G 152 TRP cc_start: 0.7325 (t60) cc_final: 0.6741 (t60) REVERT: H 32 MET cc_start: 0.7347 (ptm) cc_final: 0.7110 (ptm) REVERT: H 68 LEU cc_start: 0.6894 (tt) cc_final: 0.6537 (pp) REVERT: I 25 GLN cc_start: 0.7755 (mt0) cc_final: 0.7370 (tp40) REVERT: J 147 LYS cc_start: 0.6584 (tttt) cc_final: 0.6294 (tmtt) REVERT: K 59 GLU cc_start: 0.7054 (tp30) cc_final: 0.6794 (tp30) REVERT: L 73 ASN cc_start: 0.5536 (p0) cc_final: 0.5094 (p0) REVERT: M 130 GLU cc_start: 0.7781 (tt0) cc_final: 0.7562 (tt0) REVERT: R 86 GLN cc_start: 0.5909 (tm-30) cc_final: 0.5602 (tp-100) REVERT: S 58 MET cc_start: 0.3705 (mmm) cc_final: 0.3432 (mmm) REVERT: S 118 GLN cc_start: 0.6731 (mp10) cc_final: 0.6503 (mp10) REVERT: T 104 ASP cc_start: 0.6946 (t0) cc_final: 0.6547 (m-30) REVERT: U 44 GLU cc_start: 0.7207 (pm20) cc_final: 0.6531 (tt0) REVERT: V 56 MET cc_start: 0.6887 (mtm) cc_final: 0.6384 (tpt) REVERT: c 75 GLU cc_start: 0.3806 (pm20) cc_final: 0.3437 (pm20) REVERT: d 31 ARG cc_start: 0.7931 (ptt180) cc_final: 0.7621 (ptp90) REVERT: e 13 LYS cc_start: 0.7544 (mtmt) cc_final: 0.6965 (mttp) REVERT: e 25 SER cc_start: 0.6935 (m) cc_final: 0.6671 (m) REVERT: e 26 ASN cc_start: 0.6515 (t0) cc_final: 0.6173 (m-40) REVERT: f 109 MET cc_start: 0.5973 (tmm) cc_final: 0.5722 (tmm) outliers start: 3 outliers final: 0 residues processed: 505 average time/residue: 0.8021 time to fit residues: 712.3721 Evaluate side-chains 400 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 4.401 ------------------------------------------------------------------------------- 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: 30.0000 chunk 185 optimal weight: 5.9990 chunk 498 optimal weight: 6.9990 chunk 407 optimal weight: 30.0000 chunk 165 optimal weight: 20.0000 chunk 599 optimal weight: 10.0000 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 0.9980 chunk 594 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 480 optimal weight: 4.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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 179 ASN D 113 GLN H 13 GLN I 44 ASN I 68 GLN L 50 GLN O 105 ASN S 31 ASN T 10 GLN V 85 HIS ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN a 103 HIS b 72 HIS c 9 HIS ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 191 HIS h 215 GLN n 22 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 84105 Z= 0.185 Angle : 0.585 9.989 122449 Z= 0.297 Chirality : 0.036 0.369 15194 Planarity : 0.005 0.061 8634 Dihedral : 23.285 179.880 34536 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.02 % Favored : 93.96 % Rotamer: Outliers : 0.07 % Allowed : 5.24 % 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: -1.57 (0.12), residues: 4821 helix: 0.28 (0.13), residues: 1492 sheet: -1.20 (0.18), residues: 733 loop : -1.82 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP L 64 HIS 0.005 0.001 HIS P 94 PHE 0.023 0.002 PHE e 52 TYR 0.029 0.002 TYR O 38 ARG 0.006 0.001 ARG e 22 *********************** 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 510 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 507 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 MET cc_start: 0.8296 (mtp) cc_final: 0.7898 (ttm) REVERT: C 169 MET cc_start: 0.7814 (mtm) cc_final: 0.7457 (mtp) REVERT: C 229 MET cc_start: 0.6765 (tmm) cc_final: 0.6544 (tmm) REVERT: C 230 GLU cc_start: 0.6499 (pt0) cc_final: 0.6101 (pt0) REVERT: D 73 MET cc_start: 0.5939 (tmm) cc_final: 0.5645 (tmm) REVERT: D 214 LEU cc_start: 0.7965 (mp) cc_final: 0.7759 (mp) REVERT: E 148 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7097 (tppt) REVERT: F 39 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7717 (tpp-160) REVERT: G 78 MET cc_start: 0.7061 (tpp) cc_final: 0.6701 (tpt) REVERT: H 32 MET cc_start: 0.7433 (ptm) cc_final: 0.7128 (ptm) REVERT: I 25 GLN cc_start: 0.7808 (mt0) cc_final: 0.7416 (tp40) REVERT: K 59 GLU cc_start: 0.7073 (tp30) cc_final: 0.6760 (tp30) REVERT: L 49 MET cc_start: 0.2643 (tpp) cc_final: 0.2403 (tpp) REVERT: L 73 ASN cc_start: 0.5556 (p0) cc_final: 0.5161 (p0) REVERT: O 33 VAL cc_start: 0.8228 (t) cc_final: 0.8003 (t) REVERT: Q 28 MET cc_start: 0.4673 (tpp) cc_final: 0.4403 (tpp) REVERT: R 86 GLN cc_start: 0.5917 (tm-30) cc_final: 0.5553 (tp-100) REVERT: S 93 GLN cc_start: 0.7916 (mp10) cc_final: 0.7628 (mp10) REVERT: S 118 GLN cc_start: 0.6963 (mp10) cc_final: 0.6754 (mp-120) REVERT: T 104 ASP cc_start: 0.6941 (t0) cc_final: 0.6448 (m-30) REVERT: V 56 MET cc_start: 0.6821 (mtm) cc_final: 0.6174 (tpt) REVERT: Z 74 MET cc_start: 0.6638 (ttm) cc_final: 0.6422 (ttm) REVERT: c 42 LYS cc_start: 0.6809 (mtmm) cc_final: 0.6584 (mttm) REVERT: c 75 GLU cc_start: 0.3817 (pm20) cc_final: 0.3402 (pm20) REVERT: e 13 LYS cc_start: 0.7541 (mtmt) cc_final: 0.6985 (mttp) REVERT: e 25 SER cc_start: 0.6962 (m) cc_final: 0.6752 (m) REVERT: e 26 ASN cc_start: 0.6442 (t0) cc_final: 0.6158 (m-40) REVERT: f 109 MET cc_start: 0.6219 (tmm) cc_final: 0.5823 (tmm) REVERT: g 143 LYS cc_start: 0.4025 (mmpt) cc_final: 0.2746 (tppt) outliers start: 3 outliers final: 0 residues processed: 508 average time/residue: 0.7409 time to fit residues: 654.1379 Evaluate side-chains 406 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 4.426 ------------------------------------------------------------------------------- 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: 1.9990 chunk 450 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 402 optimal weight: 7.9990 chunk 601 optimal weight: 0.4980 chunk 636 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 570 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 111 GLN B 132 GLN C 40 ASN C 163 GLN C 179 ASN D 113 GLN H 13 GLN I 126 HIS L 50 GLN M 19 ASN O 105 ASN S 31 ASN S 48 ASN U 42 HIS V 85 HIS ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN a 103 HIS b 25 ASN ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 84105 Z= 0.184 Angle : 0.582 9.820 122449 Z= 0.295 Chirality : 0.036 0.386 15194 Planarity : 0.005 0.057 8634 Dihedral : 23.266 179.725 34536 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.41 % Favored : 93.57 % Rotamer: Outliers : 0.07 % Allowed : 4.51 % Favored : 95.42 % 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: -1.45 (0.12), residues: 4821 helix: 0.46 (0.13), residues: 1497 sheet: -1.28 (0.18), residues: 742 loop : -1.77 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP L 64 HIS 0.006 0.001 HIS X 44 PHE 0.023 0.002 PHE J 166 TYR 0.021 0.002 TYR D 82 ARG 0.011 0.001 ARG U 62 *********************** 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 506 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 503 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 MET cc_start: 0.8467 (mtp) cc_final: 0.8244 (ttm) REVERT: B 193 HIS cc_start: 0.6436 (t-90) cc_final: 0.6228 (t-90) REVERT: C 169 MET cc_start: 0.7751 (mtm) cc_final: 0.7433 (mtp) REVERT: C 229 MET cc_start: 0.6725 (tmm) cc_final: 0.6509 (tmm) REVERT: C 230 GLU cc_start: 0.6510 (pt0) cc_final: 0.6235 (pt0) REVERT: D 215 MET cc_start: 0.6719 (ptm) cc_final: 0.6273 (ptm) REVERT: E 148 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7112 (tppt) REVERT: H 32 MET cc_start: 0.7477 (ptm) cc_final: 0.7214 (ptm) REVERT: I 25 GLN cc_start: 0.7872 (mt0) cc_final: 0.7425 (tp-100) REVERT: K 18 ARG cc_start: 0.7405 (mmm160) cc_final: 0.7155 (mmm160) REVERT: K 59 GLU cc_start: 0.7108 (tp30) cc_final: 0.6886 (tp30) REVERT: L 37 ASP cc_start: 0.6255 (p0) cc_final: 0.5486 (m-30) REVERT: L 73 ASN cc_start: 0.5535 (p0) cc_final: 0.5113 (p0) REVERT: R 86 GLN cc_start: 0.5902 (tm-30) cc_final: 0.5466 (tp-100) REVERT: S 58 MET cc_start: 0.3342 (mmt) cc_final: 0.3016 (mmm) REVERT: S 93 GLN cc_start: 0.7938 (mp10) cc_final: 0.7623 (mp10) REVERT: S 118 GLN cc_start: 0.6959 (mp10) cc_final: 0.6714 (mp10) REVERT: T 31 THR cc_start: 0.4183 (p) cc_final: 0.3977 (p) REVERT: T 104 ASP cc_start: 0.6929 (t0) cc_final: 0.6408 (m-30) REVERT: U 44 GLU cc_start: 0.7153 (pm20) cc_final: 0.6664 (tt0) REVERT: V 56 MET cc_start: 0.6833 (mtm) cc_final: 0.6205 (tpt) REVERT: c 11 SER cc_start: 0.6420 (p) cc_final: 0.6127 (t) REVERT: c 42 LYS cc_start: 0.7011 (mtmm) cc_final: 0.6748 (mttm) REVERT: c 75 GLU cc_start: 0.3858 (pm20) cc_final: 0.3392 (pm20) REVERT: d 31 ARG cc_start: 0.7980 (ptt180) cc_final: 0.7729 (ptp90) REVERT: e 13 LYS cc_start: 0.7486 (mtmt) cc_final: 0.6932 (mttp) REVERT: e 46 TYR cc_start: 0.7169 (m-10) cc_final: 0.6865 (m-10) REVERT: f 109 MET cc_start: 0.6265 (tmm) cc_final: 0.5798 (tmm) REVERT: h 4 GLN cc_start: 0.5729 (tp-100) cc_final: 0.5317 (mt0) REVERT: h 184 LEU cc_start: 0.2925 (pp) cc_final: 0.2615 (pt) outliers start: 3 outliers final: 0 residues processed: 504 average time/residue: 0.7369 time to fit residues: 647.1936 Evaluate side-chains 397 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 4.518 ------------------------------------------------------------------------------- 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: 3.9990 chunk 361 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 474 optimal weight: 20.0000 chunk 262 optimal weight: 20.0000 chunk 543 optimal weight: 9.9990 chunk 440 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 571 optimal weight: 9.9990 chunk 160 optimal weight: 50.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 111 GLN B 132 GLN C 163 GLN D 113 GLN H 13 GLN M 5 GLN O 105 ASN S 31 ASN S 48 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 84105 Z= 0.331 Angle : 0.758 9.654 122449 Z= 0.382 Chirality : 0.043 0.440 15194 Planarity : 0.006 0.068 8634 Dihedral : 23.537 179.667 34536 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.88 % Favored : 91.10 % Rotamer: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.33 % 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: -1.94 (0.12), residues: 4821 helix: -0.07 (0.13), residues: 1490 sheet: -1.66 (0.18), residues: 757 loop : -1.94 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP L 64 HIS 0.012 0.002 HIS C 208 PHE 0.031 0.003 PHE I 19 TYR 0.020 0.002 TYR h 246 ARG 0.010 0.001 ARG F 245 *********************** 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 473 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 471 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: C 229 MET cc_start: 0.6847 (tmm) cc_final: 0.6600 (tmm) REVERT: D 117 ARG cc_start: 0.5783 (mmp80) cc_final: 0.4853 (mmm-85) REVERT: D 215 MET cc_start: 0.6906 (ptm) cc_final: 0.6610 (ptm) REVERT: E 148 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7015 (tppt) REVERT: F 127 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7455 (mtm-85) REVERT: H 32 MET cc_start: 0.7366 (ptm) cc_final: 0.6971 (ptm) REVERT: I 25 GLN cc_start: 0.7915 (mt0) cc_final: 0.7416 (tp-100) REVERT: I 148 LEU cc_start: 0.7119 (pt) cc_final: 0.6915 (pp) REVERT: J 150 ASP cc_start: 0.6532 (m-30) cc_final: 0.6320 (p0) REVERT: K 59 GLU cc_start: 0.7237 (tp30) cc_final: 0.6899 (tp30) REVERT: L 37 ASP cc_start: 0.6266 (p0) cc_final: 0.5456 (m-30) REVERT: L 73 ASN cc_start: 0.5667 (p0) cc_final: 0.5294 (p0) REVERT: L 74 GLU cc_start: 0.6354 (pp20) cc_final: 0.6090 (tm-30) REVERT: M 37 TYR cc_start: 0.7569 (p90) cc_final: 0.7110 (p90) REVERT: O 50 ILE cc_start: 0.8430 (mm) cc_final: 0.8220 (mm) REVERT: R 86 GLN cc_start: 0.5814 (tm-30) cc_final: 0.5541 (tp-100) REVERT: S 35 CYS cc_start: 0.8670 (t) cc_final: 0.8451 (t) REVERT: U 114 GLU cc_start: 0.6159 (pm20) cc_final: 0.5794 (pm20) REVERT: V 56 MET cc_start: 0.7044 (mtm) cc_final: 0.6383 (tpt) REVERT: Z 74 MET cc_start: 0.7314 (ttm) cc_final: 0.7067 (ttt) REVERT: c 11 SER cc_start: 0.6745 (p) cc_final: 0.6420 (t) REVERT: c 75 GLU cc_start: 0.3874 (pm20) cc_final: 0.3422 (pm20) REVERT: d 31 ARG cc_start: 0.7946 (ptt180) cc_final: 0.7623 (ptp90) REVERT: e 13 LYS cc_start: 0.7476 (mtmt) cc_final: 0.6916 (mttp) REVERT: e 46 TYR cc_start: 0.7225 (m-10) cc_final: 0.6930 (m-10) REVERT: f 109 MET cc_start: 0.6016 (tmm) cc_final: 0.5432 (ppp) REVERT: g 143 LYS cc_start: 0.4116 (mmpt) cc_final: 0.3060 (tppt) REVERT: h 4 GLN cc_start: 0.5837 (tp-100) cc_final: 0.5463 (mt0) REVERT: h 184 LEU cc_start: 0.2704 (pp) cc_final: 0.2485 (pt) REVERT: n 12 ARG cc_start: 0.5872 (mtt180) cc_final: 0.5499 (ptp-170) outliers start: 2 outliers final: 0 residues processed: 472 average time/residue: 0.7438 time to fit residues: 606.0694 Evaluate side-chains 387 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 386 time to evaluate : 4.473 ------------------------------------------------------------------------------- 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: 0.8980 chunk 573 optimal weight: 10.0000 chunk 125 optimal weight: 40.0000 chunk 373 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 0.0470 chunk 529 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 334 optimal weight: 4.9990 overall best weight: 3.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 111 GLN B 131 HIS B 132 GLN B 141 ASN D 113 GLN D 178 HIS ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN J 99 ASN L 50 GLN O 105 ASN P 103 ASN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 ASN X 24 GLN Y 127 ASN a 103 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 84105 Z= 0.185 Angle : 0.606 9.909 122449 Z= 0.308 Chirality : 0.037 0.272 15194 Planarity : 0.005 0.066 8634 Dihedral : 23.406 179.715 34536 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.31 % Favored : 93.67 % Rotamer: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % 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: -1.63 (0.12), residues: 4821 helix: 0.34 (0.13), residues: 1482 sheet: -1.53 (0.18), residues: 744 loop : -1.83 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP L 64 HIS 0.007 0.001 HIS e 3 PHE 0.018 0.002 PHE Y 105 TYR 0.023 0.002 TYR D 82 ARG 0.011 0.000 ARG R 71 *********************** 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 516 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 512 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 GLN cc_start: 0.7326 (pm20) cc_final: 0.6924 (pm20) REVERT: B 177 MET cc_start: 0.6746 (tpp) cc_final: 0.6429 (tpp) REVERT: D 215 MET cc_start: 0.6890 (ptm) cc_final: 0.6668 (ptm) REVERT: E 148 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7010 (tppt) REVERT: E 167 TYR cc_start: 0.5275 (m-80) cc_final: 0.4948 (m-80) REVERT: H 32 MET cc_start: 0.7283 (ptm) cc_final: 0.6976 (ptm) REVERT: K 59 GLU cc_start: 0.7220 (tp30) cc_final: 0.6822 (tp30) REVERT: K 79 ARG cc_start: 0.8037 (tmt170) cc_final: 0.7797 (tmt170) REVERT: L 12 TYR cc_start: 0.4905 (m-10) cc_final: 0.4617 (m-10) REVERT: L 37 ASP cc_start: 0.6351 (p0) cc_final: 0.5493 (m-30) REVERT: L 73 ASN cc_start: 0.5622 (p0) cc_final: 0.5272 (p0) REVERT: O 50 ILE cc_start: 0.8525 (mm) cc_final: 0.8313 (mm) REVERT: P 124 MET cc_start: 0.6376 (mpp) cc_final: 0.6162 (mpp) REVERT: Q 100 LYS cc_start: 0.1550 (mmpt) cc_final: 0.0864 (mtpp) REVERT: R 86 GLN cc_start: 0.5951 (tm-30) cc_final: 0.5640 (tp-100) REVERT: S 58 MET cc_start: 0.3275 (mmt) cc_final: 0.2509 (mmm) REVERT: S 93 GLN cc_start: 0.7894 (mp10) cc_final: 0.7514 (mp10) REVERT: T 104 ASP cc_start: 0.6988 (t0) cc_final: 0.6658 (m-30) REVERT: V 56 MET cc_start: 0.7131 (mtm) cc_final: 0.6463 (tpt) REVERT: X 52 ILE cc_start: 0.8982 (pt) cc_final: 0.8764 (pt) REVERT: d 31 ARG cc_start: 0.7891 (ptt180) cc_final: 0.7673 (ptp90) REVERT: e 13 LYS cc_start: 0.7467 (mtmt) cc_final: 0.6887 (mttp) REVERT: e 46 TYR cc_start: 0.7143 (m-10) cc_final: 0.6814 (m-10) REVERT: f 109 MET cc_start: 0.5746 (tmm) cc_final: 0.5289 (tmm) REVERT: g 143 LYS cc_start: 0.4164 (mmpt) cc_final: 0.3250 (tppt) REVERT: h 4 GLN cc_start: 0.5817 (tp-100) cc_final: 0.5433 (mt0) REVERT: h 184 LEU cc_start: 0.2907 (pp) cc_final: 0.2408 (pt) REVERT: h 185 LYS cc_start: 0.4516 (pptt) cc_final: 0.4300 (pptt) outliers start: 4 outliers final: 0 residues processed: 513 average time/residue: 0.7473 time to fit residues: 661.9041 Evaluate side-chains 408 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 4.428 ------------------------------------------------------------------------------- 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: 5.9990 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 chunk 465 optimal weight: 7.9990 chunk 360 optimal weight: 6.9990 chunk 536 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 chunk 635 optimal weight: 0.9980 chunk 397 optimal weight: 4.9990 chunk 387 optimal weight: 8.9990 chunk 293 optimal weight: 30.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 111 GLN B 132 GLN D 113 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 81 HIS I 25 GLN J 99 ASN O 105 ASN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 HIS S 31 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 84105 Z= 0.189 Angle : 0.604 9.733 122449 Z= 0.306 Chirality : 0.037 0.401 15194 Planarity : 0.005 0.056 8634 Dihedral : 23.356 179.841 34536 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.86 % Favored : 92.12 % Rotamer: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.03 % 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: -1.54 (0.12), residues: 4821 helix: 0.44 (0.13), residues: 1491 sheet: -1.56 (0.18), residues: 750 loop : -1.78 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP L 64 HIS 0.006 0.001 HIS C 208 PHE 0.022 0.002 PHE J 166 TYR 0.022 0.002 TYR D 82 ARG 0.009 0.000 ARG Z 90 *********************** 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 489 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 486 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7647 (tp-100) REVERT: D 117 ARG cc_start: 0.5965 (mmp-170) cc_final: 0.4210 (mmm-85) REVERT: D 215 MET cc_start: 0.6860 (ptm) cc_final: 0.6607 (ptm) REVERT: E 148 LYS cc_start: 0.7981 (ttmt) cc_final: 0.6916 (tppt) REVERT: H 32 MET cc_start: 0.7276 (ptm) cc_final: 0.6972 (ptm) REVERT: K 59 GLU cc_start: 0.7241 (tp30) cc_final: 0.6816 (tp30) REVERT: L 12 TYR cc_start: 0.4990 (m-10) cc_final: 0.4694 (m-10) REVERT: L 37 ASP cc_start: 0.6159 (p0) cc_final: 0.5727 (m-30) REVERT: L 73 ASN cc_start: 0.5689 (p0) cc_final: 0.5311 (p0) REVERT: O 38 TYR cc_start: 0.7724 (m-80) cc_final: 0.7305 (m-80) REVERT: O 50 ILE cc_start: 0.8557 (mm) cc_final: 0.8336 (mm) REVERT: Q 100 LYS cc_start: 0.1495 (mmpt) cc_final: 0.0748 (mtpp) REVERT: R 86 GLN cc_start: 0.5900 (tm-30) cc_final: 0.5443 (tp-100) REVERT: S 58 MET cc_start: 0.3162 (mmt) cc_final: 0.2562 (mmm) REVERT: S 93 GLN cc_start: 0.8037 (mp10) cc_final: 0.7597 (mp10) REVERT: T 31 THR cc_start: 0.3818 (p) cc_final: 0.3577 (p) REVERT: T 104 ASP cc_start: 0.6956 (t0) cc_final: 0.6625 (m-30) REVERT: U 112 MET cc_start: 0.7162 (tpp) cc_final: 0.6717 (tpp) REVERT: U 114 GLU cc_start: 0.6255 (pm20) cc_final: 0.5877 (pm20) REVERT: V 56 MET cc_start: 0.7089 (mtm) cc_final: 0.6387 (tpt) REVERT: a 75 GLU cc_start: 0.6940 (tp30) cc_final: 0.6738 (tp30) REVERT: d 31 ARG cc_start: 0.7927 (ptt180) cc_final: 0.7706 (ptp90) REVERT: e 13 LYS cc_start: 0.7520 (mtmt) cc_final: 0.6946 (mttp) REVERT: e 38 MET cc_start: 0.7927 (ttp) cc_final: 0.7410 (mtp) REVERT: e 46 TYR cc_start: 0.7204 (m-10) cc_final: 0.6763 (m-10) REVERT: f 109 MET cc_start: 0.5834 (tmm) cc_final: 0.5338 (tmm) REVERT: g 143 LYS cc_start: 0.4307 (mmpt) cc_final: 0.3412 (tppt) REVERT: h 4 GLN cc_start: 0.5816 (tp-100) cc_final: 0.5425 (mt0) REVERT: h 185 LYS cc_start: 0.4385 (pptt) cc_final: 0.4147 (pptt) outliers start: 3 outliers final: 0 residues processed: 486 average time/residue: 0.7564 time to fit residues: 640.7881 Evaluate side-chains 396 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 4.426 ------------------------------------------------------------------------------- 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: 8.9990 chunk 253 optimal weight: 0.0040 chunk 379 optimal weight: 0.0070 chunk 191 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 403 optimal weight: 6.9990 chunk 432 optimal weight: 7.9990 chunk 314 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 20.0000 overall best weight: 3.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 132 GLN D 113 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 81 HIS J 99 ASN O 105 ASN S 31 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 GLN a 103 HIS e 26 ASN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 84105 Z= 0.182 Angle : 0.594 10.286 122449 Z= 0.301 Chirality : 0.037 0.354 15194 Planarity : 0.005 0.057 8634 Dihedral : 23.331 179.977 34536 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.05 % Favored : 92.93 % Rotamer: Outliers : 0.07 % Allowed : 1.30 % Favored : 98.62 % 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: -1.48 (0.12), residues: 4821 helix: 0.51 (0.14), residues: 1484 sheet: -1.54 (0.18), residues: 752 loop : -1.75 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP L 64 HIS 0.006 0.001 HIS C 208 PHE 0.027 0.001 PHE Y 105 TYR 0.024 0.002 TYR E 166 ARG 0.007 0.000 ARG O 124 *********************** 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 484 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 481 time to evaluate : 4.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6785 (tpp) cc_final: 0.6480 (tpp) REVERT: D 215 MET cc_start: 0.6857 (ptm) cc_final: 0.6539 (ptm) REVERT: E 148 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7476 (tmtt) REVERT: H 32 MET cc_start: 0.7277 (ptm) cc_final: 0.6962 (ptm) REVERT: K 59 GLU cc_start: 0.7237 (tp30) cc_final: 0.6810 (tp30) REVERT: L 12 TYR cc_start: 0.4847 (m-10) cc_final: 0.4571 (m-10) REVERT: L 37 ASP cc_start: 0.6212 (p0) cc_final: 0.5840 (m-30) REVERT: L 73 ASN cc_start: 0.5567 (p0) cc_final: 0.5259 (p0) REVERT: O 38 TYR cc_start: 0.7736 (m-80) cc_final: 0.7305 (m-80) REVERT: O 50 ILE cc_start: 0.8540 (mm) cc_final: 0.8315 (mm) REVERT: Q 100 LYS cc_start: 0.1468 (mmpt) cc_final: 0.0735 (mtpp) REVERT: R 86 GLN cc_start: 0.5890 (tm-30) cc_final: 0.5483 (tp-100) REVERT: S 58 MET cc_start: 0.3004 (mmt) cc_final: 0.2433 (mmm) REVERT: S 93 GLN cc_start: 0.8065 (mp10) cc_final: 0.7611 (mp10) REVERT: T 31 THR cc_start: 0.3767 (p) cc_final: 0.3547 (p) REVERT: e 13 LYS cc_start: 0.7502 (mtmt) cc_final: 0.6939 (mttp) REVERT: e 38 MET cc_start: 0.8003 (ttp) cc_final: 0.7567 (mtp) REVERT: e 46 TYR cc_start: 0.7301 (m-10) cc_final: 0.6749 (m-80) REVERT: f 109 MET cc_start: 0.5764 (tmm) cc_final: 0.5307 (tmm) REVERT: g 143 LYS cc_start: 0.4308 (mmpt) cc_final: 0.3397 (tppt) REVERT: h 4 GLN cc_start: 0.5816 (tp-100) cc_final: 0.5425 (mt0) REVERT: h 185 LYS cc_start: 0.4326 (pptt) cc_final: 0.4036 (pptt) outliers start: 3 outliers final: 0 residues processed: 482 average time/residue: 0.7320 time to fit residues: 615.4794 Evaluate side-chains 389 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 4.419 ------------------------------------------------------------------------------- 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: 20.0000 chunk 555 optimal weight: 5.9990 chunk 591 optimal weight: 30.0000 chunk 356 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 464 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 534 optimal weight: 20.0000 chunk 559 optimal weight: 6.9990 chunk 589 optimal weight: 30.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 111 GLN B 132 GLN D 113 GLN H 13 GLN H 81 HIS J 99 ASN L 7 ASN O 105 ASN S 31 ASN S 48 ASN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 HIS d 45 ASN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 22 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 84105 Z= 0.301 Angle : 0.730 13.080 122449 Z= 0.367 Chirality : 0.042 0.418 15194 Planarity : 0.006 0.077 8634 Dihedral : 23.521 179.886 34536 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.52 % Favored : 90.46 % Rotamer: Outliers : 0.12 % Allowed : 1.35 % Favored : 98.53 % 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: -1.89 (0.12), residues: 4821 helix: 0.03 (0.13), residues: 1499 sheet: -1.73 (0.18), residues: 726 loop : -1.92 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP L 64 HIS 0.007 0.002 HIS h 64 PHE 0.029 0.002 PHE J 166 TYR 0.021 0.002 TYR Z 76 ARG 0.008 0.001 ARG S 78 *********************** 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 475 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 470 time to evaluate : 4.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6580 (tpp) cc_final: 0.6356 (tpp) REVERT: C 103 MET cc_start: 0.6948 (ttt) cc_final: 0.6692 (ttt) REVERT: D 215 MET cc_start: 0.7148 (ptm) cc_final: 0.6881 (ptm) REVERT: E 148 LYS cc_start: 0.8037 (ttmt) cc_final: 0.7452 (tmtt) REVERT: E 166 TYR cc_start: 0.7497 (p90) cc_final: 0.7073 (p90) REVERT: G 88 MET cc_start: 0.3982 (mmm) cc_final: 0.3733 (mmm) REVERT: H 32 MET cc_start: 0.7217 (ptm) cc_final: 0.7010 (ptm) REVERT: J 150 ASP cc_start: 0.6590 (m-30) cc_final: 0.6312 (p0) REVERT: K 59 GLU cc_start: 0.7284 (tp30) cc_final: 0.6864 (tp30) REVERT: L 12 TYR cc_start: 0.4715 (m-10) cc_final: 0.4440 (m-10) REVERT: L 37 ASP cc_start: 0.6248 (p0) cc_final: 0.5944 (m-30) REVERT: L 73 ASN cc_start: 0.5527 (p0) cc_final: 0.5205 (p0) REVERT: M 134 LEU cc_start: 0.8430 (mp) cc_final: 0.8220 (mp) REVERT: O 38 TYR cc_start: 0.7768 (m-80) cc_final: 0.7301 (m-80) REVERT: O 50 ILE cc_start: 0.8384 (mm) cc_final: 0.8170 (mm) REVERT: Q 21 ASP cc_start: 0.6819 (p0) cc_final: 0.6563 (p0) REVERT: R 86 GLN cc_start: 0.5914 (tm-30) cc_final: 0.5552 (tp-100) REVERT: S 48 ASN cc_start: 0.7079 (m110) cc_final: 0.6858 (m-40) REVERT: S 93 GLN cc_start: 0.8176 (mp10) cc_final: 0.7603 (mp10) REVERT: T 31 THR cc_start: 0.3611 (p) cc_final: 0.3362 (p) REVERT: T 96 SER cc_start: 0.3749 (p) cc_final: 0.3461 (p) REVERT: U 5 THR cc_start: 0.5360 (p) cc_final: 0.5158 (p) REVERT: U 114 GLU cc_start: 0.6091 (pm20) cc_final: 0.5873 (pm20) REVERT: V 56 MET cc_start: 0.6687 (mtp) cc_final: 0.6329 (mtp) REVERT: d 63 ARG cc_start: 0.0258 (ttt90) cc_final: -0.0115 (mtp85) REVERT: e 13 LYS cc_start: 0.7492 (mtmt) cc_final: 0.6882 (mttp) REVERT: e 38 MET cc_start: 0.8029 (ttp) cc_final: 0.7590 (mtp) REVERT: f 109 MET cc_start: 0.5927 (tmm) cc_final: 0.5419 (tmm) REVERT: h 4 GLN cc_start: 0.5852 (tp-100) cc_final: 0.5484 (mt0) REVERT: n 12 ARG cc_start: 0.5895 (mtt180) cc_final: 0.5604 (ptp-170) outliers start: 5 outliers final: 1 residues processed: 473 average time/residue: 0.8263 time to fit residues: 690.0819 Evaluate side-chains 379 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 378 time to evaluate : 4.557 ------------------------------------------------------------------------------- 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: 0.0770 chunk 625 optimal weight: 30.0000 chunk 382 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 435 optimal weight: 9.9990 chunk 656 optimal weight: 20.0000 chunk 604 optimal weight: 0.4980 chunk 522 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 403 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN D 113 GLN F 188 ASN H 13 GLN H 155 GLN I 168 HIS J 99 ASN O 105 ASN S 31 ASN ** T 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS X 24 GLN a 103 HIS d 29 GLN e 26 ASN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 226 HIS n 22 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 84105 Z= 0.140 Angle : 0.581 11.840 122449 Z= 0.294 Chirality : 0.035 0.290 15194 Planarity : 0.005 0.093 8634 Dihedral : 23.320 179.939 34536 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.46 % Favored : 94.52 % Rotamer: Outliers : 0.07 % Allowed : 0.74 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.44 (0.12), residues: 4821 helix: 0.58 (0.14), residues: 1481 sheet: -1.48 (0.18), residues: 737 loop : -1.75 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.002 TRP L 64 HIS 0.006 0.001 HIS a 103 PHE 0.025 0.001 PHE Y 105 TYR 0.031 0.002 TYR D 248 ARG 0.009 0.001 ARG e 22 ********************** 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 511 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 508 time to evaluate : 4.464 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: B 177 MET cc_start: 0.6822 (tpp) cc_final: 0.6480 (tpp) REVERT: C 110 MET cc_start: 0.7837 (tpt) cc_final: 0.7627 (tpp) REVERT: E 148 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7532 (tmtt) REVERT: F 87 MET cc_start: 0.7703 (tpp) cc_final: 0.7461 (tpt) REVERT: G 78 MET cc_start: 0.7037 (tpp) cc_final: 0.6484 (tpp) REVERT: H 32 MET cc_start: 0.7402 (ptm) cc_final: 0.7038 (ptm) REVERT: J 101 ILE cc_start: 0.8467 (mm) cc_final: 0.8262 (mm) REVERT: K 59 GLU cc_start: 0.7324 (tp30) cc_final: 0.6841 (tp30) REVERT: K 143 ASN cc_start: 0.8220 (m-40) cc_final: 0.7859 (m-40) REVERT: L 12 TYR cc_start: 0.4493 (m-10) cc_final: 0.4252 (m-10) REVERT: L 37 ASP cc_start: 0.6330 (p0) cc_final: 0.5898 (m-30) REVERT: L 73 ASN cc_start: 0.5415 (p0) cc_final: 0.5032 (p0) REVERT: M 134 LEU cc_start: 0.8308 (mp) cc_final: 0.8074 (mp) REVERT: O 38 TYR cc_start: 0.7576 (m-80) cc_final: 0.7158 (m-80) REVERT: O 50 ILE cc_start: 0.8491 (mm) cc_final: 0.8265 (mm) REVERT: Q 21 ASP cc_start: 0.7143 (p0) cc_final: 0.6710 (p0) REVERT: R 86 GLN cc_start: 0.5807 (tm-30) cc_final: 0.5353 (tp-100) REVERT: S 58 MET cc_start: 0.2729 (mmt) cc_final: 0.2372 (mmm) REVERT: S 93 GLN cc_start: 0.8114 (mp10) cc_final: 0.7651 (mp10) REVERT: U 44 GLU cc_start: 0.7057 (pm20) cc_final: 0.6835 (tt0) REVERT: U 114 GLU cc_start: 0.6181 (pm20) cc_final: 0.5979 (pm20) REVERT: V 56 MET cc_start: 0.6582 (mtp) cc_final: 0.5811 (tpt) REVERT: X 61 ILE cc_start: 0.8481 (mp) cc_final: 0.8053 (mm) REVERT: Z 74 MET cc_start: 0.6755 (ttm) cc_final: 0.6290 (ttm) REVERT: c 75 GLU cc_start: 0.4234 (pm20) cc_final: 0.3920 (pm20) REVERT: e 13 LYS cc_start: 0.7394 (mtmt) cc_final: 0.6822 (mttp) REVERT: f 109 MET cc_start: 0.5655 (tmm) cc_final: 0.5237 (tmm) REVERT: g 143 LYS cc_start: 0.4540 (mmpt) cc_final: 0.3685 (tppt) REVERT: h 4 GLN cc_start: 0.5743 (tp-100) cc_final: 0.5445 (mt0) REVERT: n 1 MET cc_start: 0.7372 (mpp) cc_final: 0.7016 (mmp) outliers start: 3 outliers final: 0 residues processed: 509 average time/residue: 0.7292 time to fit residues: 644.6620 Evaluate side-chains 378 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 6.033 ------------------------------------------------------------------------------- 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: 8.9990 chunk 556 optimal weight: 7.9990 chunk 160 optimal weight: 40.0000 chunk 482 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 537 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 111 GLN B 131 HIS B 132 GLN D 113 GLN H 13 GLN J 99 ASN O 105 ASN S 29 HIS S 31 ASN S 48 ASN ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS ** W 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 33 GLN X 24 GLN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 16 HIS a 103 HIS e 26 ASN e 45 GLN ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.078466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.065038 restraints weight = 451027.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064834 restraints weight = 339445.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065273 restraints weight = 245598.623| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 84105 Z= 0.271 Angle : 0.700 13.030 122449 Z= 0.353 Chirality : 0.040 0.374 15194 Planarity : 0.006 0.072 8634 Dihedral : 23.416 179.974 34536 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.42 % Favored : 90.56 % Rotamer: Outliers : 0.07 % Allowed : 0.66 % Favored : 99.26 % 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: -1.76 (0.12), residues: 4821 helix: 0.15 (0.13), residues: 1493 sheet: -1.64 (0.18), residues: 761 loop : -1.85 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP L 64 HIS 0.011 0.001 HIS C 208 PHE 0.027 0.002 PHE E 24 TYR 0.023 0.002 TYR e 34 ARG 0.024 0.001 ARG L 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12246.99 seconds wall clock time: 217 minutes 17.79 seconds (13037.79 seconds total)