Starting phenix.real_space_refine on Mon Sep 30 02:41:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/09_2024/7syn_25534.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/09_2024/7syn_25534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/09_2024/7syn_25534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/09_2024/7syn_25534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/09_2024/7syn_25534.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7syn_25534/09_2024/7syn_25534.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 81 residue(s): 0.10s 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': 113, 'rna3p_pur': 754, 'rna3p_pyr': 687} Link IDs: {'rna2p': 255, 'rna3p': 1441} 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 92.888 128.480 132.515 1.00 40.42 S ATOM 69352 SG CYS b 26 95.819 129.317 135.400 1.00 46.80 S ATOM 69735 SG CYS b 74 95.119 126.037 134.169 1.00 39.58 S ATOM 69754 SG CYS b 77 95.025 128.105 135.939 1.00 41.97 S ATOM 72396 SG CYS g 121 141.261 111.137 244.385 1.00128.07 S ATOM 72432 SG CYS g 126 139.659 108.910 242.798 1.00135.44 S ATOM 72550 SG CYS g 141 141.802 112.282 240.878 1.00152.31 S ATOM 72569 SG CYS g 144 138.910 111.855 241.491 1.00150.33 S Time building chain proxies: 33.40, per 1000 atoms: 0.42 Number of scatterers: 78761 At special positions: 0 Unit cell: (236.55, 195.7, 264.1, 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: 14.86 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 23 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 26 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN g 200 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 121 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " 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: 157 helices and 60 sheets defined 35.2% alpha, 17.8% beta 477 base pairs and 878 stacking pairs defined. Time for finding SS restraints: 26.98 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.970A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 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 68 removed outlier: 3.673A pdb=" N THR B 54 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) 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 130 through 138 removed outlier: 3.822A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.633A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.576A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.960A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.658A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 6.102A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 54 through 60 removed outlier: 3.521A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 60' Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 97 through 111 removed outlier: 3.588A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY E 111 " --> pdb=" O TYR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 130 removed outlier: 3.868A pdb=" N GLY E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 37 through 41 removed outlier: 3.838A pdb=" N CYS F 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 59 through 67 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 67 through 75 removed outlier: 3.535A pdb=" N SER G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 3.707A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 removed outlier: 3.506A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 114 " --> pdb=" O GLN G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 Processing helix chain 'G' and resid 168 through 173 Processing helix chain 'G' and resid 173 through 178 removed outlier: 3.526A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 183 Processing helix chain 'G' and resid 187 through 203 removed outlier: 4.191A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 28 removed outlier: 3.619A pdb=" N TYR H 28 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 236 Processing helix chain 'I' and resid 17 through 34 Processing helix chain 'I' and resid 36 through 40 Processing helix chain 'I' and resid 68 through 73 Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.021A pdb=" N VAL I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.972A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.969A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 118 Processing helix chain 'J' and resid 132 through 139 removed outlier: 3.737A pdb=" N LEU J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.708A pdb=" N LYS J 148 " --> pdb=" O LYS J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 178 through 183 removed outlier: 3.613A pdb=" N CYS J 182 " --> pdb=" O ARG J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 207 Processing helix chain 'K' and resid 21 through 36 removed outlier: 3.618A pdb=" N LEU K 25 " --> pdb=" O GLU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.239A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 Processing helix chain 'K' and resid 93 through 100 Processing helix chain 'K' and resid 101 through 107 Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 172 through 186 removed outlier: 3.827A pdb=" N LYS K 176 " --> pdb=" O ARG K 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 17 removed outlier: 3.514A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 Processing helix chain 'L' and resid 72 through 84 Processing helix chain 'M' and resid 48 through 53 Processing helix chain 'N' and resid 15 through 29 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 60 through 70 removed outlier: 3.701A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 90 Processing helix chain 'N' and resid 119 through 130 removed outlier: 4.225A pdb=" N VAL N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.781A pdb=" N VAL O 33 " --> pdb=" O THR O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.648A pdb=" N GLY O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL O 52 " --> pdb=" O SER O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.999A pdb=" N VAL O 66 " --> pdb=" O GLN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 105 removed outlier: 4.349A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN O 105 " --> pdb=" O HIS O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'P' and resid 58 through 62 removed outlier: 3.583A pdb=" N VAL P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 62' Processing helix chain 'P' and resid 64 through 68 Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.164A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.954A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 47 removed outlier: 3.965A pdb=" N ARG Q 47 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 Processing helix chain 'Q' and resid 108 through 112 removed outlier: 4.093A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) 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 59 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 60 through 65 removed outlier: 4.155A pdb=" N GLY R 65 " --> pdb=" O GLU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.658A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.854A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 39 Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 75 through 84 Processing helix chain 'S' and resid 99 through 108 removed outlier: 3.651A pdb=" N LEU S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.784A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.597A pdb=" N VAL T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.591A pdb=" N TYR T 77 " --> pdb=" O PRO T 74 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 74 through 78' Processing helix chain 'T' and resid 80 through 84 removed outlier: 3.555A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 118 Processing helix chain 'T' and resid 119 through 128 Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.709A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 37 removed outlier: 4.511A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL U 37 " --> pdb=" O VAL U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 72 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 28 through 46 removed outlier: 3.779A pdb=" N LEU V 32 " --> pdb=" O ASN V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.801A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.652A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 77 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 45 Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.592A pdb=" N ASN X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 119 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: 4.023A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 94 Processing helix chain 'Y' and resid 130 through 136 Processing helix chain 'Z' and resid 36 through 49 Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 87 through 95 removed outlier: 3.695A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 116 Processing helix chain 'Z' and resid 120 through 125 removed outlier: 4.089A 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 78 Processing helix chain 'a' and resid 80 through 94 Processing helix chain 'b' and resid 48 through 56 removed outlier: 4.636A pdb=" N ASP b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 Processing helix chain 'e' and resid 3 through 8 removed outlier: 4.418A pdb=" N TRP e 8 " --> pdb=" O GLN e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 Processing helix chain 'e' and resid 40 through 46 Processing helix chain 'e' and resid 46 through 51 removed outlier: 3.680A pdb=" N ILE e 50 " --> pdb=" O TYR e 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 105 through 115 removed outlier: 4.100A pdb=" N GLN f 110 " --> pdb=" O LYS f 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 105 Processing helix chain 'n' and resid 2 through 25 Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.008A pdb=" N ILE B 48 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.334A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 147 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.686A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 13.418A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 216 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 67 removed outlier: 3.501A pdb=" N LEU C 86 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 13.418A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 216 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C 142 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 104 through 116 removed outlier: 5.544A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 127 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 137 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.742A pdb=" N VAL D 205 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 224 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 40 removed outlier: 3.505A pdb=" N ILE E 49 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU E 85 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU E 89 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.704A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET E 189 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 137 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.704A pdb=" N VAL E 136 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET E 189 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 137 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 223 through 226 removed outlier: 6.698A pdb=" N VAL h 176 " --> pdb=" O LYS h 185 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN h 187 " --> pdb=" O VAL h 174 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL h 174 " --> pdb=" O ASN h 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.511A pdb=" N ILE F 92 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU F 97 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.209A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.508A pdb=" N LYS F 122 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 159 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 217 through 221 removed outlier: 6.799A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 229 through 230 removed outlier: 3.516A pdb=" N LYS F 230 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS F 233 " --> pdb=" O LYS F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 123 through 126 removed outlier: 8.699A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE d 42 " --> pdb=" O VAL d 32 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N CYS d 27 " --> pdb=" O GLY d 19 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY d 19 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR d 15 " --> pdb=" O ARG d 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.515A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.770A pdb=" N ASN H 56 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 77 removed outlier: 3.813A pdb=" N LYS H 93 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 160 through 164 removed outlier: 3.549A pdb=" N LYS H 160 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS H 164 " --> pdb=" O LYS H 168 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS H 168 " --> pdb=" O LYS H 164 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 48 through 52 removed outlier: 3.658A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 185 through 188 removed outlier: 8.394A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU I 153 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE I 144 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS I 155 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS I 142 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS I 157 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL X 25 " --> pdb=" O VAL X 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 42 through 47 removed outlier: 6.680A 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 66 removed outlier: 3.519A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG J 74 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG J 77 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.643A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 20 through 24 removed outlier: 3.693A pdb=" N ALA L 23 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 72 through 79 removed outlier: 6.981A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL M 142 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY M 129 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS M 144 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 91 through 96 removed outlier: 4.035A pdb=" N ARG M 101 " --> pdb=" O ILE M 96 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 31 through 32 removed outlier: 3.588A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 52 through 53 removed outlier: 7.153A pdb=" N LEU N 52 " --> pdb=" O VAL N 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'P' and resid 52 through 57 removed outlier: 7.345A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG P 55 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL P 42 " --> pdb=" O ARG P 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR P 40 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP P 39 " --> pdb=" O SER P 36 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE P 95 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE P 129 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU P 97 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP P 131 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 76 through 78 removed outlier: 6.073A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR Q 78 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR Q 101 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 12 through 15 removed outlier: 7.020A pdb=" N LYS R 33 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N VAL R 72 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 97 through 98 removed outlier: 3.984A pdb=" N VAL S 98 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'T' and resid 12 through 15 Processing sheet with id=AE1, first strand: chain 'U' and resid 81 through 83 removed outlier: 3.904A pdb=" N GLY U 81 " --> pdb=" O SER U 93 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER U 93 " --> pdb=" O GLY U 81 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS U 91 " --> pdb=" O GLN U 83 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE3, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.557A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 54 through 55 removed outlier: 4.038A pdb=" N THR V 25 " --> pdb=" O GLU V 111 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU V 111 " --> pdb=" O THR V 25 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 15 through 16 removed outlier: 4.145A pdb=" N ARG W 15 " --> pdb=" O ILE W 24 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 32 through 39 removed outlier: 4.094A pdb=" N GLU W 38 " --> pdb=" O GLN W 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.772A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE X 128 " --> pdb=" O GLY X 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 71 through 74 removed outlier: 3.772A pdb=" N LYS X 71 " --> pdb=" O PHE X 130 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE X 130 " --> pdb=" O LYS X 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE X 128 " --> pdb=" O GLY X 73 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL X 103 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE X 128 " --> pdb=" O PHE X 101 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE X 101 " --> pdb=" O PHE X 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 128 through 129 removed outlier: 5.039A pdb=" N VAL Y 122 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA Y 103 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS Y 124 " --> pdb=" O LEU Y 101 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 10.855A pdb=" N PHE Y 120 " --> pdb=" O LYS Y 80 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR Y 82 " --> pdb=" O PHE Y 120 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL Y 122 " --> pdb=" O THR Y 82 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE Y 84 " --> pdb=" O VAL Y 122 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N LYS Y 124 " --> pdb=" O PHE Y 84 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 6 through 15 removed outlier: 3.783A pdb=" N ARG Z 8 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 99 through 102 removed outlier: 3.676A pdb=" N SER a 101 " --> pdb=" O ILE a 108 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF4, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.652A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 32 through 33 Processing sheet with id=AF6, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.743A pdb=" N MET e 38 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 106 through 108 removed outlier: 3.689A pdb=" N SER g 115 " --> pdb=" O LYS g 107 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 139 through 140 removed outlier: 3.761A pdb=" N HIS g 139 " --> pdb=" O TYR g 148 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR g 148 " --> pdb=" O HIS g 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'h' and resid 5 through 11 removed outlier: 6.245A pdb=" N LEU h 7 " --> pdb=" O GLN h 311 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN h 311 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY h 9 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL h 307 " --> pdb=" O LEU h 11 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY h 301 " --> pdb=" O THR h 287 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 18 through 22 removed outlier: 6.652A pdb=" N ALA h 34 " --> pdb=" O THR h 19 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE h 21 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU h 32 " --> pdb=" O ILE h 21 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER h 33 " --> pdb=" O ILE h 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE h 41 " --> pdb=" O SER h 33 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.636A pdb=" N ALA h 78 " --> pdb=" O TRP h 90 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG h 99 " --> pdb=" O LEU h 89 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP h 91 " --> pdb=" O THR h 97 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR h 97 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 108 through 113 removed outlier: 3.586A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE h 129 " --> pdb=" O THR h 141 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR h 141 " --> pdb=" O ILE h 129 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU h 131 " --> pdb=" O LYS h 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 151 through 155 Processing sheet with id=AG5, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.654A pdb=" N THR h 197 " --> pdb=" O GLY h 210 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 239 through 241 removed outlier: 3.627A pdb=" N LEU h 248 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) 1454 hydrogen bonds defined for protein. 4122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1206 hydrogen bonds 2044 hydrogen bond angles 0 basepair planarities 477 basepair parallelities 878 stacking parallelities Total time for adding SS restraints: 62.19 Time building geometry restraints manager: 18.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 17358 1.34 - 1.46: 27996 1.46 - 1.58: 34773 1.58 - 1.70: 3704 1.70 - 1.82: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" C ASP E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.19e-02 7.06e+03 4.56e+00 bond pdb=" C VAL a 62 " pdb=" N PRO a 63 " ideal model delta sigma weight residual 1.337 1.355 -0.019 9.80e-03 1.04e+04 3.59e+00 bond pdb=" CB PRO Y 62 " pdb=" CG PRO Y 62 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" CG PRO E 219 " pdb=" CD PRO E 219 " ideal model delta sigma weight residual 1.503 1.444 0.059 3.40e-02 8.65e+02 3.01e+00 bond pdb=" N PRO Y 62 " pdb=" CA PRO Y 62 " ideal model delta sigma weight residual 1.479 1.455 0.024 1.56e-02 4.11e+03 2.28e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 121281 2.07 - 4.15: 1035 4.15 - 6.22: 111 6.22 - 8.30: 17 8.30 - 10.37: 5 Bond angle restraints: 122449 Sorted by residual: angle pdb=" CA PRO Y 62 " pdb=" N PRO Y 62 " pdb=" CD PRO Y 62 " ideal model delta sigma weight residual 112.00 103.40 8.60 1.40e+00 5.10e-01 3.77e+01 angle pdb=" CA PRO E 219 " pdb=" N PRO E 219 " pdb=" CD PRO E 219 " ideal model delta sigma weight residual 112.00 105.89 6.11 1.40e+00 5.10e-01 1.90e+01 angle pdb=" N PRO E 219 " pdb=" CD PRO E 219 " pdb=" CG PRO E 219 " ideal model delta sigma weight residual 103.20 96.98 6.22 1.50e+00 4.44e-01 1.72e+01 angle pdb=" C THR Z 50 " pdb=" N THR Z 51 " pdb=" CA THR Z 51 " ideal model delta sigma weight residual 120.67 125.97 -5.30 1.34e+00 5.57e-01 1.56e+01 angle pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " pdb=" P U 2 689 " ideal model delta sigma weight residual 120.20 125.91 -5.71 1.50e+00 4.44e-01 1.45e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 48536 35.87 - 71.74: 4550 71.74 - 107.62: 591 107.62 - 143.49: 9 143.49 - 179.36: 28 Dihedral angle restraints: 53714 sinusoidal: 39658 harmonic: 14056 Sorted by residual: dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual -160.00 17.15 -177.15 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 10.70 -170.70 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C 21303 " pdb=" C1' C 21303 " pdb=" N1 C 21303 " pdb=" C2 C 21303 " ideal model delta sinusoidal sigma weight residual 200.00 36.43 163.57 1 1.50e+01 4.44e-03 8.36e+01 ... (remaining 53711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 14199 0.061 - 0.123: 947 0.123 - 0.184: 44 0.184 - 0.246: 3 0.246 - 0.307: 1 Chirality restraints: 15194 Sorted by residual: chirality pdb=" C1' U 21203 " pdb=" O4' U 21203 " pdb=" C2' U 21203 " pdb=" N1 U 21203 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1' A 2 531 " pdb=" O4' A 2 531 " pdb=" C2' A 2 531 " pdb=" N9 A 2 531 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' U z 160 " pdb=" C4' U z 160 " pdb=" O3' U z 160 " pdb=" C2' U z 160 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.19 2.00e-01 2.50e+01 9.46e-01 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN Y 61 " -0.077 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO Y 62 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO Y 62 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO Y 62 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 218 " -0.057 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO E 219 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 219 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 219 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 23 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO C 24 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 24 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 24 " 0.041 5.00e-02 4.00e+02 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 3335 2.67 - 3.23: 68448 3.23 - 3.79: 138897 3.79 - 4.34: 182351 4.34 - 4.90: 263792 Nonbonded interactions: 656823 Sorted by model distance: nonbonded pdb=" O2' G 21550 " pdb=" O2 C 21558 " model vdw 2.115 3.040 nonbonded pdb=" OP2 C 2 98 " pdb=" O2' A 2 426 " model vdw 2.127 3.040 nonbonded pdb=" O2' A 21822 " pdb=" NZ LYS Y 60 " model vdw 2.154 3.120 nonbonded pdb=" OG SER B 2 " pdb=" OE1 GLU B 56 " model vdw 2.156 3.040 nonbonded pdb=" O2 U 2 372 " pdb=" O2' G 2 394 " model vdw 2.159 3.040 ... (remaining 656818 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.680 Check model and map are aligned: 0.480 Set scattering table: 0.580 Process input model: 194.060 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.220 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 205.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 : 0.002 0.087 84105 Z= 0.115 Angle : 0.495 10.371 122449 Z= 0.257 Chirality : 0.031 0.307 15194 Planarity : 0.004 0.112 8634 Dihedral : 21.988 179.362 44648 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.83 (0.12), residues: 4821 helix: 1.35 (0.14), residues: 1484 sheet: -0.80 (0.19), residues: 767 loop : -1.69 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP T 127 HIS 0.009 0.001 HIS C 208 PHE 0.021 0.001 PHE T 83 TYR 0.024 0.001 TYR Q 17 ARG 0.008 0.000 ARG L 55 *********************** 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 756 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 756 time to evaluate : 4.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 183 LEU cc_start: 0.7653 (mt) cc_final: 0.7438 (mt) REVERT: E 74 GLN cc_start: 0.7085 (mp10) cc_final: 0.6747 (mp10) REVERT: F 118 GLU cc_start: 0.6570 (tt0) cc_final: 0.6293 (tt0) REVERT: F 143 ASP cc_start: 0.6409 (p0) cc_final: 0.5700 (p0) REVERT: G 140 ASP cc_start: 0.6871 (m-30) cc_final: 0.6546 (m-30) REVERT: H 120 ASP cc_start: 0.6603 (t0) cc_final: 0.6142 (p0) REVERT: J 182 CYS cc_start: 0.7586 (p) cc_final: 0.7293 (p) REVERT: O 117 LEU cc_start: 0.8756 (mt) cc_final: 0.8455 (mt) REVERT: R 20 THR cc_start: 0.6695 (p) cc_final: 0.6483 (p) REVERT: S 4 VAL cc_start: 0.7358 (t) cc_final: 0.7133 (t) REVERT: S 116 ASN cc_start: 0.7290 (t0) cc_final: 0.7069 (t0) REVERT: T 82 TRP cc_start: 0.5434 (p-90) cc_final: 0.4760 (p-90) REVERT: U 12 GLN cc_start: 0.6681 (tp40) cc_final: 0.6446 (tp40) REVERT: U 13 GLU cc_start: 0.6113 (tp30) cc_final: 0.5413 (tp30) REVERT: U 131 LEU cc_start: 0.8099 (tp) cc_final: 0.7878 (tp) REVERT: U 138 VAL cc_start: 0.6689 (t) cc_final: 0.6215 (t) REVERT: W 53 TYR cc_start: 0.7151 (m-10) cc_final: 0.6783 (m-80) REVERT: W 72 LEU cc_start: 0.7828 (mt) cc_final: 0.7625 (mt) REVERT: W 76 ASP cc_start: 0.6558 (m-30) cc_final: 0.5666 (m-30) REVERT: X 51 GLU cc_start: 0.7947 (tp30) cc_final: 0.7557 (tp30) REVERT: a 49 LEU cc_start: 0.5503 (tp) cc_final: 0.5162 (tt) REVERT: d 26 GLN cc_start: 0.6843 (pm20) cc_final: 0.6393 (pm20) REVERT: f 91 LYS cc_start: 0.7673 (mppt) cc_final: 0.7448 (mtmm) REVERT: h 142 VAL cc_start: 0.5274 (m) cc_final: 0.4972 (p) outliers start: 0 outliers final: 0 residues processed: 756 average time/residue: 0.7359 time to fit residues: 956.1538 Evaluate side-chains 595 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 595 time to evaluate : 4.663 ------------------------------------------------------------------------------- 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: 4.9990 chunk 499 optimal weight: 0.5980 chunk 277 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 336 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 516 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 314 optimal weight: 0.9990 chunk 384 optimal weight: 4.9990 chunk 598 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN G 36 GLN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN K 132 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 45 GLN f 88 GLN h 64 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 84105 Z= 0.169 Angle : 0.559 11.403 122449 Z= 0.277 Chirality : 0.034 0.302 15194 Planarity : 0.004 0.066 8634 Dihedral : 23.177 179.417 34536 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.30 % Allowed : 9.27 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.79 (0.12), residues: 4821 helix: 1.33 (0.14), residues: 1506 sheet: -0.71 (0.18), residues: 824 loop : -1.69 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP h 219 HIS 0.010 0.001 HIS C 208 PHE 0.029 0.001 PHE B 90 TYR 0.025 0.001 TYR Q 17 ARG 0.006 0.000 ARG e 12 *********************** 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 697 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 642 time to evaluate : 5.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.6670 (mttp) cc_final: 0.6317 (mtmm) REVERT: B 47 TYR cc_start: 0.8069 (m-80) cc_final: 0.7849 (m-80) REVERT: B 183 LEU cc_start: 0.7800 (mt) cc_final: 0.7490 (mt) REVERT: D 152 ARG cc_start: 0.6959 (mmt180) cc_final: 0.6491 (tpp80) REVERT: D 156 ILE cc_start: 0.8651 (mt) cc_final: 0.8407 (mm) REVERT: E 74 GLN cc_start: 0.7093 (mp10) cc_final: 0.6435 (mp10) REVERT: E 87 TYR cc_start: 0.4321 (m-10) cc_final: 0.3797 (m-80) REVERT: I 72 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6677 (t80) REVERT: I 120 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7553 (mmt-90) REVERT: I 181 THR cc_start: 0.7916 (p) cc_final: 0.7635 (p) REVERT: J 111 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7252 (tm-30) REVERT: J 182 CYS cc_start: 0.7626 (p) cc_final: 0.7304 (p) REVERT: K 175 ARG cc_start: 0.7252 (ptp-110) cc_final: 0.6982 (ptm-80) REVERT: L 80 ARG cc_start: 0.4460 (ptp-170) cc_final: 0.4233 (mtm-85) REVERT: Q 85 ILE cc_start: 0.5500 (mt) cc_final: 0.5267 (mt) REVERT: Q 111 MET cc_start: 0.5314 (mmp) cc_final: 0.5103 (mmt) REVERT: T 82 TRP cc_start: 0.5452 (p-90) cc_final: 0.4537 (p-90) REVERT: T 85 ASN cc_start: 0.5617 (t0) cc_final: 0.5365 (t0) REVERT: U 13 GLU cc_start: 0.6233 (tp30) cc_final: 0.5543 (tp30) REVERT: U 105 GLN cc_start: 0.7560 (mm110) cc_final: 0.7118 (mm-40) REVERT: X 88 LYS cc_start: 0.8545 (mmtp) cc_final: 0.7743 (ttmm) REVERT: X 115 GLU cc_start: 0.8099 (tt0) cc_final: 0.7782 (tt0) REVERT: h 42 MET cc_start: 0.5307 (ttp) cc_final: 0.4779 (mtp) outliers start: 55 outliers final: 35 residues processed: 671 average time/residue: 0.7587 time to fit residues: 888.3539 Evaluate side-chains 615 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 579 time to evaluate : 4.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Z residue 13 MET Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain h residue 14 HIS 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: 7.9990 chunk 498 optimal weight: 5.9990 chunk 407 optimal weight: 0.0980 chunk 165 optimal weight: 20.0000 chunk 599 optimal weight: 30.0000 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 0.6980 chunk 594 optimal weight: 0.0020 chunk 204 optimal weight: 3.9990 chunk 480 optimal weight: 20.0000 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 91 ASN ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN h 14 HIS h 64 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 84105 Z= 0.145 Angle : 0.516 10.395 122449 Z= 0.257 Chirality : 0.033 0.307 15194 Planarity : 0.004 0.061 8634 Dihedral : 23.076 179.882 34536 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.94 % Allowed : 12.78 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.74 (0.12), residues: 4821 helix: 1.31 (0.14), residues: 1516 sheet: -0.62 (0.18), residues: 828 loop : -1.64 (0.12), residues: 2477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 127 HIS 0.019 0.001 HIS Y 23 PHE 0.024 0.001 PHE B 32 TYR 0.023 0.001 TYR Q 37 ARG 0.006 0.000 ARG V 83 *********************** 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 696 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 614 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.6540 (mttp) cc_final: 0.6130 (mtmm) REVERT: B 47 TYR cc_start: 0.8012 (m-80) cc_final: 0.7692 (m-80) REVERT: B 183 LEU cc_start: 0.7687 (mt) cc_final: 0.7374 (mt) REVERT: C 198 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6683 (tm-30) REVERT: E 31 GLU cc_start: 0.5626 (pp20) cc_final: 0.5422 (pp20) REVERT: E 87 TYR cc_start: 0.4318 (m-80) cc_final: 0.4006 (m-80) REVERT: G 176 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6802 (mp0) REVERT: I 72 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6734 (t80) REVERT: I 181 THR cc_start: 0.7968 (p) cc_final: 0.7763 (p) REVERT: J 111 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7177 (tm-30) REVERT: J 182 CYS cc_start: 0.7638 (p) cc_final: 0.7293 (p) REVERT: K 175 ARG cc_start: 0.7307 (ptp-110) cc_final: 0.7075 (ptm-80) REVERT: L 2 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5652 (pp) REVERT: T 28 PHE cc_start: 0.5607 (m-80) cc_final: 0.5404 (m-10) REVERT: T 82 TRP cc_start: 0.5456 (p-90) cc_final: 0.4379 (p-90) REVERT: T 85 ASN cc_start: 0.5793 (t0) cc_final: 0.5493 (t0) REVERT: T 124 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.7032 (tpt-90) REVERT: U 13 GLU cc_start: 0.6228 (tp30) cc_final: 0.5526 (tp30) REVERT: W 56 CYS cc_start: 0.8241 (p) cc_final: 0.7758 (p) REVERT: W 76 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6668 (p0) REVERT: X 88 LYS cc_start: 0.8572 (mmtp) cc_final: 0.7800 (ttmm) REVERT: d 26 GLN cc_start: 0.6950 (pm20) cc_final: 0.6506 (pm20) outliers start: 82 outliers final: 51 residues processed: 653 average time/residue: 0.7203 time to fit residues: 815.4294 Evaluate side-chains 627 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 572 time to evaluate : 4.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain X residue 41 MET Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain h residue 14 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 3.9990 chunk 450 optimal weight: 0.6980 chunk 311 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 402 optimal weight: 7.9990 chunk 601 optimal weight: 0.7980 chunk 636 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 570 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 165 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS M 5 GLN P 32 HIS Q 41 GLN ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN f 88 GLN ** h 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 84105 Z= 0.193 Angle : 0.554 10.475 122449 Z= 0.275 Chirality : 0.034 0.262 15194 Planarity : 0.004 0.060 8634 Dihedral : 23.060 179.904 34536 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.51 % Allowed : 15.01 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.83 (0.12), residues: 4821 helix: 1.15 (0.14), residues: 1524 sheet: -0.63 (0.18), residues: 838 loop : -1.67 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP h 219 HIS 0.019 0.001 HIS h 14 PHE 0.019 0.002 PHE V 80 TYR 0.018 0.001 TYR Q 37 ARG 0.008 0.000 ARG V 83 *********************** 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 698 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 592 time to evaluate : 4.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.6634 (mttp) cc_final: 0.6231 (mtmm) REVERT: B 47 TYR cc_start: 0.8026 (m-80) cc_final: 0.7608 (m-80) REVERT: D 152 ARG cc_start: 0.7077 (mmt180) cc_final: 0.6697 (tpp80) REVERT: E 31 GLU cc_start: 0.5600 (pp20) cc_final: 0.5341 (pp20) REVERT: E 68 GLU cc_start: 0.5650 (pt0) cc_final: 0.5266 (mm-30) REVERT: E 87 TYR cc_start: 0.4341 (m-80) cc_final: 0.4096 (m-80) REVERT: F 121 TYR cc_start: 0.8466 (p90) cc_final: 0.8227 (p90) REVERT: G 176 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6888 (mp0) REVERT: I 32 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.5683 (tmm) REVERT: I 72 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6711 (t80) REVERT: J 111 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7436 (tm-30) REVERT: J 182 CYS cc_start: 0.7672 (p) cc_final: 0.7317 (p) REVERT: K 175 ARG cc_start: 0.7325 (ptp-110) cc_final: 0.7087 (ptm-80) REVERT: L 2 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5790 (pp) REVERT: O 36 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7663 (mm-40) REVERT: Q 85 ILE cc_start: 0.5324 (mt) cc_final: 0.5057 (mt) REVERT: T 82 TRP cc_start: 0.5505 (p-90) cc_final: 0.4079 (p-90) REVERT: U 13 GLU cc_start: 0.6221 (tp30) cc_final: 0.5577 (tp30) REVERT: V 62 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: V 81 GLN cc_start: 0.7282 (mt0) cc_final: 0.6547 (mt0) REVERT: W 76 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6783 (p0) REVERT: d 26 GLN cc_start: 0.6971 (pm20) cc_final: 0.6537 (pm20) REVERT: h 42 MET cc_start: 0.5215 (ttp) cc_final: 0.4724 (mtp) outliers start: 106 outliers final: 69 residues processed: 648 average time/residue: 0.7163 time to fit residues: 806.8871 Evaluate side-chains 637 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 564 time to evaluate : 4.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain M residue 5 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain W residue 10 ASP Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain X residue 19 LYS Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain X residue 41 MET Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 13 MET Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain h residue 14 HIS Chi-restraints excluded: chain h residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 530 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 474 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 543 optimal weight: 6.9990 chunk 440 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 325 optimal weight: 6.9990 chunk 571 optimal weight: 0.0000 chunk 160 optimal weight: 30.0000 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN C 101 HIS ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 GLN J 99 ASN K 124 HIS ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN V 92 HIS X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 89 HIS ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN h 14 HIS ** h 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 84105 Z= 0.260 Angle : 0.630 10.099 122449 Z= 0.313 Chirality : 0.037 0.241 15194 Planarity : 0.005 0.063 8634 Dihedral : 23.168 179.986 34536 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.20 % Allowed : 15.87 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.11 (0.12), residues: 4821 helix: 0.84 (0.14), residues: 1523 sheet: -0.65 (0.18), residues: 825 loop : -1.84 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 23 HIS 0.016 0.002 HIS h 14 PHE 0.029 0.002 PHE D 236 TYR 0.024 0.002 TYR R 96 ARG 0.007 0.001 ARG V 83 *********************** 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 726 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 591 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.6761 (mttp) cc_final: 0.6336 (mtmm) REVERT: B 99 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8179 (mt) REVERT: E 31 GLU cc_start: 0.5669 (pp20) cc_final: 0.5346 (pp20) REVERT: I 72 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6710 (t80) REVERT: J 111 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7521 (tm-30) REVERT: J 145 ILE cc_start: 0.5961 (pt) cc_final: 0.5731 (pt) REVERT: J 182 CYS cc_start: 0.7694 (p) cc_final: 0.7301 (p) REVERT: J 198 TYR cc_start: 0.8934 (m-80) cc_final: 0.8716 (m-80) REVERT: L 2 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5741 (pp) REVERT: L 80 ARG cc_start: 0.4375 (ptp-170) cc_final: 0.4120 (tpp80) REVERT: Q 93 MET cc_start: 0.3915 (mmp) cc_final: 0.3680 (mmp) REVERT: R 116 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: U 13 GLU cc_start: 0.6243 (tp30) cc_final: 0.5633 (tp30) REVERT: W 76 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6795 (p0) REVERT: Y 60 LYS cc_start: 0.7138 (mttm) cc_final: 0.6774 (mmtp) REVERT: b 55 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6718 (pm20) REVERT: d 26 GLN cc_start: 0.6985 (pm20) cc_final: 0.6659 (pm20) REVERT: n 9 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7432 (ptp-110) REVERT: n 20 MET cc_start: 0.6068 (ppp) cc_final: 0.5865 (ppp) outliers start: 135 outliers final: 90 residues processed: 668 average time/residue: 0.7236 time to fit residues: 836.1688 Evaluate side-chains 644 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 548 time to evaluate : 4.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 186 ASN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain U residue 134 ILE Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain X residue 19 LYS Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 61 GLN Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 13 MET Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain h residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 214 optimal weight: 8.9990 chunk 573 optimal weight: 5.9990 chunk 125 optimal weight: 30.0000 chunk 373 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 637 optimal weight: 0.1980 chunk 529 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 334 optimal weight: 6.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN D 120 GLN F 232 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS N 75 ASN ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 GLN ** h 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 84105 Z= 0.232 Angle : 0.605 10.946 122449 Z= 0.302 Chirality : 0.037 0.236 15194 Planarity : 0.005 0.064 8634 Dihedral : 23.182 179.875 34536 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.92 % Allowed : 17.36 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.15 (0.12), residues: 4821 helix: 0.79 (0.13), residues: 1533 sheet: -0.76 (0.18), residues: 824 loop : -1.82 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 23 HIS 0.011 0.001 HIS C 124 PHE 0.028 0.002 PHE U 21 TYR 0.019 0.002 TYR c 31 ARG 0.012 0.001 ARG V 83 *********************** 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 702 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 579 time to evaluate : 4.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.6735 (mttp) cc_final: 0.6324 (mtmm) REVERT: B 130 ASP cc_start: 0.7680 (m-30) cc_final: 0.7211 (t0) REVERT: E 107 TYR cc_start: 0.6282 (m-10) cc_final: 0.6044 (m-80) REVERT: F 90 ILE cc_start: 0.9165 (tt) cc_final: 0.8949 (mm) REVERT: F 143 ASP cc_start: 0.7212 (p0) cc_final: 0.6559 (p0) REVERT: G 176 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6981 (mp0) REVERT: I 72 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6784 (t80) REVERT: J 111 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7448 (tm-30) REVERT: J 182 CYS cc_start: 0.7773 (p) cc_final: 0.7375 (p) REVERT: K 65 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5047 (mm-30) REVERT: T 82 TRP cc_start: 0.5607 (p-90) cc_final: 0.4205 (p-90) REVERT: T 124 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6874 (tpt-90) REVERT: U 13 GLU cc_start: 0.6197 (tp30) cc_final: 0.5629 (tp30) REVERT: U 96 SER cc_start: 0.6627 (t) cc_final: 0.6346 (m) REVERT: W 56 CYS cc_start: 0.8338 (p) cc_final: 0.7883 (p) REVERT: W 76 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6760 (p0) REVERT: Y 60 LYS cc_start: 0.7157 (mttm) cc_final: 0.6786 (mmtp) REVERT: Z 74 MET cc_start: 0.8531 (ttm) cc_final: 0.8282 (mtm) REVERT: a 61 GLU cc_start: 0.3838 (OUTLIER) cc_final: 0.3584 (mp0) REVERT: c 6 ASP cc_start: 0.6046 (t0) cc_final: 0.5795 (p0) REVERT: d 26 GLN cc_start: 0.6893 (pm20) cc_final: 0.6618 (pm20) REVERT: n 9 ARG cc_start: 0.7963 (ttp-170) cc_final: 0.7444 (ptp-110) outliers start: 123 outliers final: 89 residues processed: 654 average time/residue: 0.7212 time to fit residues: 826.6251 Evaluate side-chains 646 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 552 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain H residue 83 CYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain X residue 19 LYS Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 13 MET Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain h residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 363 optimal weight: 3.9990 chunk 465 optimal weight: 7.9990 chunk 360 optimal weight: 5.9990 chunk 536 optimal weight: 5.9990 chunk 356 optimal weight: 5.9990 chunk 635 optimal weight: 20.0000 chunk 397 optimal weight: 6.9990 chunk 387 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 141 ASN D 120 GLN F 232 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 HIS L 28 HIS L 44 HIS ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 85 ASN X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 GLN h 14 HIS ** h 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 84105 Z= 0.280 Angle : 0.663 9.823 122449 Z= 0.330 Chirality : 0.039 0.248 15194 Planarity : 0.005 0.062 8634 Dihedral : 23.276 179.763 34536 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.56 % Allowed : 17.93 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.36 (0.12), residues: 4821 helix: 0.58 (0.13), residues: 1524 sheet: -0.83 (0.18), residues: 830 loop : -1.95 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 23 HIS 0.012 0.001 HIS Y 23 PHE 0.030 0.002 PHE D 236 TYR 0.036 0.002 TYR B 156 ARG 0.009 0.001 ARG W 61 *********************** 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 711 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 561 time to evaluate : 4.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.6769 (mttp) cc_final: 0.6401 (mtmm) REVERT: C 157 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6640 (mt0) REVERT: F 143 ASP cc_start: 0.7381 (p0) cc_final: 0.6820 (p0) REVERT: G 18 LYS cc_start: 0.6769 (mmmt) cc_final: 0.6335 (mptt) REVERT: G 175 ASP cc_start: 0.6466 (p0) cc_final: 0.5928 (p0) REVERT: G 176 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7094 (mp0) REVERT: I 72 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6742 (t80) REVERT: J 111 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7407 (tm-30) REVERT: J 182 CYS cc_start: 0.7825 (p) cc_final: 0.7410 (p) REVERT: Q 79 HIS cc_start: 0.4947 (OUTLIER) cc_final: 0.3287 (t-90) REVERT: T 124 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6950 (tpt-90) REVERT: U 13 GLU cc_start: 0.6121 (tp30) cc_final: 0.5526 (tp30) REVERT: U 96 SER cc_start: 0.6547 (t) cc_final: 0.6311 (m) REVERT: W 76 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6817 (p0) REVERT: a 61 GLU cc_start: 0.3869 (OUTLIER) cc_final: 0.3615 (mp0) REVERT: c 6 ASP cc_start: 0.6084 (t0) cc_final: 0.5818 (p0) REVERT: d 26 GLN cc_start: 0.6869 (pm20) cc_final: 0.6666 (pm20) REVERT: e 31 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7188 (mm) REVERT: n 9 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7710 (ptp-170) outliers start: 150 outliers final: 111 residues processed: 661 average time/residue: 0.7108 time to fit residues: 821.6173 Evaluate side-chains 660 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 542 time to evaluate : 4.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain H residue 83 CYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 186 ASN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 MET Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 24 ILE Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain X residue 19 LYS Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 61 GLN Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 13 MET Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain h residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 392 optimal weight: 5.9990 chunk 253 optimal weight: 0.1980 chunk 379 optimal weight: 30.0000 chunk 191 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 403 optimal weight: 8.9990 chunk 432 optimal weight: 20.0000 chunk 314 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 0.9980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 232 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 91 ASN ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 84105 Z= 0.211 Angle : 0.604 10.764 122449 Z= 0.302 Chirality : 0.037 0.261 15194 Planarity : 0.005 0.063 8634 Dihedral : 23.229 179.708 34536 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.51 % Allowed : 18.90 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.24 (0.12), residues: 4821 helix: 0.74 (0.13), residues: 1524 sheet: -0.82 (0.18), residues: 835 loop : -1.88 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 23 HIS 0.012 0.001 HIS Y 23 PHE 0.026 0.002 PHE U 21 TYR 0.024 0.002 TYR M 55 ARG 0.011 0.000 ARG V 83 *********************** 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 719 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 571 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.6709 (mttp) cc_final: 0.6342 (mtmm) REVERT: F 143 ASP cc_start: 0.7333 (p0) cc_final: 0.6736 (p0) REVERT: G 176 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6811 (mp0) REVERT: I 72 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6758 (t80) REVERT: J 111 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7467 (tm-30) REVERT: J 145 ILE cc_start: 0.5803 (pt) cc_final: 0.5565 (pt) REVERT: J 182 CYS cc_start: 0.7828 (p) cc_final: 0.7412 (p) REVERT: K 65 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.4963 (mm-30) REVERT: L 2 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5753 (pp) REVERT: L 47 LYS cc_start: 0.4215 (mttm) cc_final: 0.3986 (mttm) REVERT: T 71 MET cc_start: 0.6566 (ppp) cc_final: 0.5740 (tmm) REVERT: T 124 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6879 (tpt-90) REVERT: U 13 GLU cc_start: 0.6123 (tp30) cc_final: 0.5567 (tp30) REVERT: W 76 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6716 (p0) REVERT: a 47 LEU cc_start: 0.5286 (mp) cc_final: 0.5049 (mp) REVERT: a 61 GLU cc_start: 0.3833 (OUTLIER) cc_final: 0.3555 (mp0) REVERT: c 6 ASP cc_start: 0.6091 (t0) cc_final: 0.5732 (p0) REVERT: e 31 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.6979 (mm) REVERT: e 44 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.5202 (ttp80) REVERT: n 9 ARG cc_start: 0.7907 (ttp-170) cc_final: 0.7424 (ptp-110) outliers start: 148 outliers final: 117 residues processed: 666 average time/residue: 0.7204 time to fit residues: 840.6547 Evaluate side-chains 671 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 546 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain H residue 83 CYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 186 ASN Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 MET Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain X residue 19 LYS Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 61 GLN Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 13 MET Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain g residue 132 MET Chi-restraints excluded: chain h residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 577 optimal weight: 5.9990 chunk 608 optimal weight: 0.8980 chunk 555 optimal weight: 6.9990 chunk 591 optimal weight: 9.9990 chunk 356 optimal weight: 0.5980 chunk 257 optimal weight: 9.9990 chunk 464 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 534 optimal weight: 7.9990 chunk 559 optimal weight: 10.0000 chunk 589 optimal weight: 2.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 GLN F 232 ASN ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS L 77 GLN ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 120 HIS X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 26 GLN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 HIS ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 84105 Z= 0.155 Angle : 0.553 9.966 122449 Z= 0.279 Chirality : 0.034 0.240 15194 Planarity : 0.004 0.063 8634 Dihedral : 23.122 179.960 34536 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.75 % Allowed : 19.73 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.02 (0.12), residues: 4821 helix: 0.97 (0.14), residues: 1524 sheet: -0.74 (0.18), residues: 828 loop : -1.76 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 55 HIS 0.011 0.001 HIS Y 23 PHE 0.026 0.001 PHE U 21 TYR 0.027 0.001 TYR B 156 ARG 0.012 0.000 ARG V 83 *********************** 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 708 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 592 time to evaluate : 4.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.6636 (mttp) cc_final: 0.6242 (mtmm) REVERT: B 47 TYR cc_start: 0.7866 (m-80) cc_final: 0.7592 (m-80) REVERT: B 130 ASP cc_start: 0.7568 (m-30) cc_final: 0.7178 (t0) REVERT: C 157 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6711 (mt0) REVERT: D 276 THR cc_start: 0.4984 (p) cc_final: 0.4735 (p) REVERT: F 143 ASP cc_start: 0.7166 (p0) cc_final: 0.6580 (p0) REVERT: G 176 GLU cc_start: 0.7564 (mt-10) cc_final: 0.6885 (mp0) REVERT: I 72 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6787 (t80) REVERT: J 111 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7444 (tm-30) REVERT: J 145 ILE cc_start: 0.5776 (pt) cc_final: 0.5548 (pt) REVERT: J 154 LYS cc_start: 0.5605 (mtmm) cc_final: 0.5331 (mtmm) REVERT: J 182 CYS cc_start: 0.7728 (p) cc_final: 0.7320 (p) REVERT: K 65 GLU cc_start: 0.5745 (OUTLIER) cc_final: 0.5002 (mm-30) REVERT: L 2 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5698 (pp) REVERT: L 47 LYS cc_start: 0.4278 (mttm) cc_final: 0.3975 (mttm) REVERT: Q 28 MET cc_start: 0.4058 (tpt) cc_final: 0.3366 (tpp) REVERT: R 145 TYR cc_start: 0.6685 (m-10) cc_final: 0.6175 (m-80) REVERT: T 71 MET cc_start: 0.6346 (ppp) cc_final: 0.5328 (tmm) REVERT: T 82 TRP cc_start: 0.5763 (p-90) cc_final: 0.4440 (p-90) REVERT: T 124 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6811 (tpt-90) REVERT: U 13 GLU cc_start: 0.6053 (tp30) cc_final: 0.5487 (tp30) REVERT: V 80 PHE cc_start: 0.8095 (m-80) cc_final: 0.7855 (m-80) REVERT: W 56 CYS cc_start: 0.8396 (p) cc_final: 0.7866 (p) REVERT: W 76 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6709 (p0) REVERT: Y 60 LYS cc_start: 0.7084 (mttm) cc_final: 0.6673 (mmtp) REVERT: Z 74 MET cc_start: 0.8548 (ttm) cc_final: 0.8267 (mtm) REVERT: c 6 ASP cc_start: 0.6024 (t0) cc_final: 0.5692 (p0) REVERT: e 31 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7135 (mm) REVERT: e 44 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5233 (ttp80) REVERT: h 64 HIS cc_start: 0.6750 (OUTLIER) cc_final: 0.6529 (t-170) REVERT: n 9 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7518 (ptp-110) outliers start: 116 outliers final: 85 residues processed: 662 average time/residue: 0.7317 time to fit residues: 847.0770 Evaluate side-chains 659 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 565 time to evaluate : 4.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 MET Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain U residue 85 ASN Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 81 LYS Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 61 GLN Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 13 MET Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain g residue 132 MET Chi-restraints excluded: chain h residue 64 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 388 optimal weight: 6.9990 chunk 625 optimal weight: 9.9990 chunk 382 optimal weight: 0.6980 chunk 296 optimal weight: 1.9990 chunk 435 optimal weight: 20.0000 chunk 656 optimal weight: 20.0000 chunk 604 optimal weight: 4.9990 chunk 522 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 403 optimal weight: 10.0000 chunk 320 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS L 77 GLN ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN f 88 GLN h 14 HIS ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 84105 Z= 0.230 Angle : 0.611 11.699 122449 Z= 0.304 Chirality : 0.036 0.238 15194 Planarity : 0.005 0.063 8634 Dihedral : 23.140 179.983 34536 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.63 % Allowed : 20.02 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.13 (0.12), residues: 4821 helix: 0.82 (0.14), residues: 1526 sheet: -0.74 (0.18), residues: 814 loop : -1.82 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP h 43 HIS 0.014 0.001 HIS Y 23 PHE 0.031 0.002 PHE U 21 TYR 0.021 0.002 TYR M 55 ARG 0.010 0.001 ARG V 83 ********************** 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 685 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 574 time to evaluate : 5.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 LYS cc_start: 0.6663 (mttp) cc_final: 0.6328 (mtmm) REVERT: B 47 TYR cc_start: 0.7911 (m-80) cc_final: 0.7585 (m-10) REVERT: C 157 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6764 (mt0) REVERT: D 276 THR cc_start: 0.5017 (p) cc_final: 0.4800 (p) REVERT: F 143 ASP cc_start: 0.7315 (p0) cc_final: 0.6739 (p0) REVERT: G 176 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6749 (mp0) REVERT: I 72 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6698 (t80) REVERT: J 111 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7419 (tm-30) REVERT: J 145 ILE cc_start: 0.5829 (pt) cc_final: 0.5602 (pt) REVERT: J 182 CYS cc_start: 0.7761 (p) cc_final: 0.7327 (p) REVERT: K 65 GLU cc_start: 0.5754 (OUTLIER) cc_final: 0.4982 (mm-30) REVERT: L 2 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5675 (pp) REVERT: L 47 LYS cc_start: 0.4310 (mttm) cc_final: 0.4015 (mttm) REVERT: Q 28 MET cc_start: 0.4148 (tpt) cc_final: 0.3539 (tpp) REVERT: R 145 TYR cc_start: 0.6761 (m-10) cc_final: 0.6314 (m-80) REVERT: T 71 MET cc_start: 0.6346 (ppp) cc_final: 0.5509 (tmm) REVERT: T 124 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6915 (tpt-90) REVERT: U 13 GLU cc_start: 0.6143 (tp30) cc_final: 0.5523 (tp30) REVERT: V 80 PHE cc_start: 0.8173 (m-80) cc_final: 0.7928 (m-80) REVERT: W 76 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6772 (p0) REVERT: a 61 GLU cc_start: 0.3856 (OUTLIER) cc_final: 0.3516 (mp0) REVERT: c 6 ASP cc_start: 0.6019 (t0) cc_final: 0.5816 (p0) REVERT: e 31 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7119 (mm) REVERT: n 9 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7740 (ptp-170) outliers start: 111 outliers final: 94 residues processed: 645 average time/residue: 0.7145 time to fit residues: 809.9399 Evaluate side-chains 654 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 552 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 176 ILE Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 79 HIS Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 93 MET Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 26 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 124 ARG Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 104 ILE Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain X residue 19 LYS Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 58 GLU Chi-restraints excluded: chain Y residue 61 GLN Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain Z residue 13 MET Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 84 HIS Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 121 THR Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain g residue 132 MET Chi-restraints excluded: chain h residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 415 optimal weight: 9.9990 chunk 556 optimal weight: 3.9990 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 537 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS L 44 HIS L 77 GLN ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 HIS ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 215 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.097860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.076777 restraints weight = 253193.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.076507 restraints weight = 183930.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.077039 restraints weight = 154952.519| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 84105 Z= 0.275 Angle : 0.658 9.895 122449 Z= 0.328 Chirality : 0.038 0.246 15194 Planarity : 0.005 0.061 8634 Dihedral : 23.230 179.930 34536 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.87 % Allowed : 20.07 % Favored : 77.06 % 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: -1.32 (0.12), residues: 4821 helix: 0.65 (0.13), residues: 1519 sheet: -0.81 (0.18), residues: 816 loop : -1.94 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 43 HIS 0.013 0.001 HIS Y 23 PHE 0.028 0.002 PHE D 236 TYR 0.025 0.002 TYR E 87 ARG 0.010 0.001 ARG W 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14156.38 seconds wall clock time: 248 minutes 43.24 seconds (14923.24 seconds total)