Starting phenix.real_space_refine on Mon Sep 30 04:40:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sym_25533/09_2024/7sym_25533.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sym_25533/09_2024/7sym_25533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sym_25533/09_2024/7sym_25533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sym_25533/09_2024/7sym_25533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sym_25533/09_2024/7sym_25533.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sym_25533/09_2024/7sym_25533.cif" } resolution = 4.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 98 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 78761 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 36227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36227 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 142, 'rna2p_pyr': 114, 'rna3p_pur': 755, 'rna3p_pyr': 686} 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 93.989 132.283 137.800 1.00 68.82 S ATOM 69352 SG CYS b 26 96.925 132.514 141.146 1.00 71.31 S ATOM 69735 SG CYS b 74 95.460 130.178 139.421 1.00 64.63 S ATOM 69754 SG CYS b 77 95.925 131.859 141.735 1.00 70.66 S ATOM 72396 SG CYS g 121 150.598 104.583 243.994 1.00302.27 S ATOM 72432 SG CYS g 126 148.843 103.379 242.854 1.00307.70 S ATOM 72550 SG CYS g 141 151.099 105.906 241.113 1.00298.59 S ATOM 72569 SG CYS g 144 147.491 106.970 242.835 1.00300.10 S Time building chain proxies: 31.45, per 1000 atoms: 0.40 Number of scatterers: 78761 At special positions: 0 Unit cell: (232.75, 194.75, 261.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 180 16.00 P 1858 15.00 O 19829 8.00 N 14495 7.00 C 42397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.89 Conformation dependent library (CDL) restraints added in 4.1 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 121 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 126 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 141 " pdb="ZN ZN g 200 " - pdb=" SG CYS g 144 " 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: 143 helices and 58 sheets defined 33.6% alpha, 16.3% beta 450 base pairs and 941 stacking pairs defined. Time for finding SS restraints: 23.17 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.853A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.624A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 4.723A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 removed outlier: 3.754A pdb=" N VAL B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.842A pdb=" N LEU B 201 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'C' and resid 23 through 26 removed outlier: 3.588A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.909A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 177 removed outlier: 4.266A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.941A pdb=" N ILE C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.560A pdb=" N HIS C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.602A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 91 through 98 removed outlier: 4.037A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 160 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.850A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 removed outlier: 5.998A pdb=" N ASP D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 111 removed outlier: 3.794A pdb=" N GLN E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 129 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.581A pdb=" N VAL F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 247 through 263 removed outlier: 4.375A pdb=" N GLY F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 46 Processing helix chain 'G' and resid 61 through 66 removed outlier: 3.539A pdb=" N ALA G 64 " --> pdb=" O PHE G 61 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN G 65 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS G 66 " --> pdb=" O LYS G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 66' Processing helix chain 'G' and resid 67 through 77 removed outlier: 4.051A pdb=" N MET G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 104 removed outlier: 4.025A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR G 104 " --> pdb=" O ILE G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 removed outlier: 3.524A pdb=" N LEU G 112 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN G 114 " --> pdb=" O GLN G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 162 removed outlier: 3.522A pdb=" N VAL G 147 " --> pdb=" O PRO G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 180 removed outlier: 4.187A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 203 removed outlier: 3.646A pdb=" N LYS G 191 " --> pdb=" O SER G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 27 removed outlier: 4.474A pdb=" N THR H 26 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 237 removed outlier: 3.566A pdb=" N LEU H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) 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 74 removed outlier: 3.606A pdb=" N PHE I 72 " --> pdb=" O GLN I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 87 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.854A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 181 Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.771A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.725A pdb=" N LYS J 147 " --> pdb=" O LYS J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 4.218A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE K 53 " --> pdb=" O THR K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 93 through 100 removed outlier: 3.770A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU K 98 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY K 99 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 107 removed outlier: 3.773A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 150 through 154 removed outlier: 3.789A pdb=" N GLN K 154 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 167 removed outlier: 3.935A pdb=" N GLY K 167 " --> pdb=" O PRO K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 186 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.559A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE L 9 " --> pdb=" O LYS L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 56 removed outlier: 3.505A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 53 removed outlier: 3.821A pdb=" N ILE M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) 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: 3.917A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.530A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL N 89 " --> pdb=" O LEU N 85 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY N 90 " --> pdb=" O GLY N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 129 Processing helix chain 'O' and resid 29 through 43 Processing helix chain 'O' and resid 46 through 57 Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.551A pdb=" N VAL O 66 " --> pdb=" O GLN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 Processing helix chain 'O' and resid 85 through 105 removed outlier: 3.995A pdb=" N ARG O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 132 removed outlier: 3.592A pdb=" N LYS O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG O 127 " --> pdb=" O HIS O 123 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 89 Processing helix chain 'P' and resid 110 through 123 removed outlier: 3.699A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY P 123 " --> pdb=" O LEU P 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 3.729A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 43 Processing helix chain 'Q' and resid 54 through 66 Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.616A pdb=" N MET Q 89 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 112 removed outlier: 4.080A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 119 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 77 through 99 removed outlier: 4.116A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 116 removed outlier: 4.326A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP R 116 " --> pdb=" O LEU R 112 " (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 38 Processing helix chain 'S' and resid 44 through 64 Processing helix chain 'S' and resid 99 through 110 removed outlier: 3.820A pdb=" N LEU S 109 " --> pdb=" O MET S 105 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP S 110 " --> pdb=" O LEU S 106 " (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 39 through 48 removed outlier: 4.057A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL T 44 " --> pdb=" O TYR T 40 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA T 48 " --> pdb=" O VAL T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 80 through 84 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: 4.397A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.971A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 97 through 110 Processing helix chain 'U' and resid 124 through 143 Processing helix chain 'V' and resid 28 through 46 removed outlier: 3.835A pdb=" N LEU V 32 " --> pdb=" O ASN V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.646A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 62 Processing helix chain 'W' and resid 64 through 77 removed outlier: 3.998A pdb=" N GLY W 77 " --> pdb=" O ALA W 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 21 removed outlier: 3.645A pdb=" N ASP X 9 " --> pdb=" O ASN X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 44 removed outlier: 3.657A pdb=" N VAL X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 93 removed outlier: 3.519A pdb=" N TRP X 89 " --> pdb=" O ASP X 85 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.809A pdb=" N LEU Y 13 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 39 removed outlier: 4.156A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 48 removed outlier: 4.029A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 87 through 95 removed outlier: 3.965A pdb=" N LEU Z 91 " --> pdb=" O PRO Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 117 removed outlier: 3.743A pdb=" N VAL Z 117 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 126 removed outlier: 3.543A pdb=" N GLY Z 126 " --> pdb=" O LYS Z 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.554A pdb=" N TYR a 55 " --> pdb=" O ASP a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 77 Processing helix chain 'a' and resid 80 through 95 Processing helix chain 'b' and resid 49 through 56 Processing helix chain 'b' and resid 75 through 81 Processing helix chain 'b' and resid 88 through 94 removed outlier: 3.584A pdb=" N ARG b 92 " --> pdb=" O ARG b 89 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS b 93 " --> pdb=" O GLU b 90 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP b 94 " --> pdb=" O ALA b 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.608A pdb=" N LYS c 18 " --> pdb=" O GLU c 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 8 removed outlier: 4.130A pdb=" N TRP e 8 " --> pdb=" O GLN e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.688A pdb=" N GLY e 35 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 46 Processing helix chain 'e' and resid 46 through 51 removed outlier: 3.869A pdb=" N GLY e 51 " --> pdb=" O ALA e 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 107 through 115 removed outlier: 4.396A pdb=" N TYR f 111 " --> pdb=" O ARG f 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 105 Processing helix chain 'n' and resid 2 through 25 removed outlier: 3.686A pdb=" N ARG n 6 " --> pdb=" O ARG n 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.343A 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: 6.603A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 159 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.588A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 33 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 47 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 86 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.793A pdb=" N GLY C 141 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 142 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP C 209 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 124 through 128 Processing sheet with id=AA6, first strand: chain 'D' and resid 103 through 115 removed outlier: 5.970A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 142 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 128 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 140 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 185 through 188 removed outlier: 3.883A pdb=" N CYS D 188 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 191 " --> pdb=" O CYS D 188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 205 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR D 224 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.908A pdb=" N LEU E 51 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL E 37 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE E 49 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL E 39 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU E 47 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU E 85 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU E 89 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 52 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 155 removed outlier: 3.577A pdb=" N ILE E 184 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 186 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 223 through 226 removed outlier: 5.425A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU h 173 " --> pdb=" O GLY h 169 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY h 169 " --> pdb=" O LEU h 173 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS h 153 " --> pdb=" O CYS h 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.449A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.821A pdb=" N ASN F 98 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.014A pdb=" N ILE F 102 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 121 through 124 removed outlier: 7.238A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR F 170 " --> pdb=" O GLN F 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 126 through 131 removed outlier: 3.618A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 217 through 221 removed outlier: 7.564A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU F 180 " --> pdb=" O ILE F 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AC1, first strand: chain 'G' and resid 123 through 126 removed outlier: 3.512A pdb=" N ASP G 124 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN G 137 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS d 27 " --> pdb=" O GLY d 19 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLY d 19 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR d 15 " --> pdb=" O ARG d 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.975A pdb=" N ILE H 5 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 114 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL H 50 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL H 36 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.975A pdb=" N ILE H 5 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL H 108 " --> pdb=" O ASN H 56 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 72 through 77 Processing sheet with id=AC5, first strand: chain 'I' and resid 48 through 53 removed outlier: 3.671A pdb=" N LYS I 49 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE I 61 " --> pdb=" O LYS I 49 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE I 51 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA I 59 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 184 through 188 removed outlier: 6.483A pdb=" N ARG I 152 " --> pdb=" O ASP I 184 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE X 52 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS X 60 " --> pdb=" O ILE X 53 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.795A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 37 through 38 removed outlier: 6.187A pdb=" N LYS J 37 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS J 54 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL J 46 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 62 through 67 removed outlier: 3.576A pdb=" N PHE J 65 " --> pdb=" O ARG J 74 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP J 80 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL J 82 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU J 171 " --> pdb=" O ILE J 104 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY J 187 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AD2, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AD3, first strand: chain 'M' and resid 72 through 79 removed outlier: 7.372A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER M 110 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL M 142 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N HIS M 112 " --> pdb=" O VAL M 142 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LYS M 144 " --> pdb=" O HIS M 112 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 91 through 95 Processing sheet with id=AD5, first strand: chain 'N' and resid 49 through 53 removed outlier: 3.898A pdb=" N CYS N 50 " --> pdb=" O ASN N 75 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE N 77 " --> pdb=" O CYS N 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 52 through 56 removed outlier: 4.010A pdb=" N CYS P 54 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL P 44 " --> pdb=" O CYS P 54 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU P 93 " --> pdb=" O ILE P 126 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG P 128 " --> pdb=" O LEU P 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 76 through 77 removed outlier: 6.165A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 11 through 13 removed outlier: 3.671A pdb=" N THR R 20 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LYS R 33 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL R 72 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 97 through 98 Processing sheet with id=AE1, first strand: chain 'T' and resid 12 through 14 Processing sheet with id=AE2, first strand: chain 'U' and resid 80 through 82 removed outlier: 3.689A pdb=" N GLY U 81 " --> pdb=" O SER U 93 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER U 93 " --> pdb=" O GLY U 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'U' and resid 113 through 115 removed outlier: 3.542A pdb=" N LYS U 122 " --> pdb=" O GLU U 114 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 20 through 26 Processing sheet with id=AE5, first strand: chain 'V' and resid 49 through 50 removed outlier: 3.942A pdb=" N LYS V 49 " --> pdb=" O HIS V 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE V 84 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 63 through 66 removed outlier: 3.689A pdb=" N THR V 65 " --> pdb=" O ASP V 78 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 35 through 39 removed outlier: 4.004A pdb=" N GLU W 38 " --> pdb=" O GLN W 49 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 71 through 74 removed outlier: 4.049A pdb=" N PHE X 128 " --> pdb=" O GLY X 73 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 71 through 74 removed outlier: 4.049A pdb=" N PHE X 128 " --> pdb=" O GLY X 73 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 80 through 82 removed outlier: 4.157A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 6 through 15 removed outlier: 3.583A pdb=" N THR Z 6 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET Z 23 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL Z 27 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LYS Z 68 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR Z 62 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 67 through 68 removed outlier: 7.292A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL a 100 " --> pdb=" O ILE a 108 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR a 110 " --> pdb=" O LYS a 98 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS a 98 " --> pdb=" O THR a 110 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 37 through 43 removed outlier: 3.633A pdb=" N VAL b 40 " --> pdb=" O VAL b 69 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG b 42 " --> pdb=" O LEU b 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 44 through 47 removed outlier: 3.971A pdb=" N ASP c 34 " --> pdb=" O ARG c 80 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 119 through 120 removed outlier: 3.590A pdb=" N ARG g 119 " --> pdb=" O MET g 132 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 5 through 6 removed outlier: 3.843A pdb=" N THR h 6 " --> pdb=" O GLN h 311 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 10 through 11 removed outlier: 3.566A pdb=" N SER h 288 " --> pdb=" O GLY h 301 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 18 through 22 removed outlier: 6.493A pdb=" N ALA h 34 " --> pdb=" O THR h 19 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE h 21 " --> pdb=" O LEU h 32 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU h 32 " --> pdb=" O ILE h 21 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TRP h 43 " --> pdb=" O ILE h 31 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE h 40 " --> pdb=" O ALA h 58 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA h 58 " --> pdb=" O ILE h 40 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET h 42 " --> pdb=" O GLN h 56 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.548A pdb=" N ALA h 78 " --> pdb=" O TRP h 90 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG h 88 " --> pdb=" O SER h 80 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 108 through 113 removed outlier: 3.935A pdb=" N ILE h 120 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS h 130 " --> pdb=" O SER h 122 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.514A pdb=" N THR h 199 " --> pdb=" O ALA h 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER h 209 " --> pdb=" O MET h 217 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET h 217 " --> pdb=" O SER h 209 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 239 through 241 removed outlier: 4.016A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) 1361 hydrogen bonds defined for protein. 3891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1146 hydrogen bonds 1944 hydrogen bond angles 0 basepair planarities 450 basepair parallelities 941 stacking parallelities Total time for adding SS restraints: 56.74 Time building geometry restraints manager: 16.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15756 1.33 - 1.46: 29898 1.46 - 1.58: 34473 1.58 - 1.70: 3704 1.70 - 1.82: 274 Bond restraints: 84105 Sorted by residual: bond pdb=" C GLU V 107 " pdb=" N PRO V 108 " ideal model delta sigma weight residual 1.337 1.364 -0.027 9.80e-03 1.04e+04 7.68e+00 bond pdb=" CB PRO R 124 " pdb=" CG PRO R 124 " ideal model delta sigma weight residual 1.492 1.609 -0.117 5.00e-02 4.00e+02 5.44e+00 bond pdb=" C GLN B 132 " pdb=" N PRO B 133 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.28e-02 6.10e+03 4.57e+00 bond pdb=" CA ASP F 176 " pdb=" CB ASP F 176 " ideal model delta sigma weight residual 1.535 1.573 -0.038 1.90e-02 2.77e+03 4.05e+00 bond pdb=" C LEU R 52 " pdb=" N GLU R 53 " ideal model delta sigma weight residual 1.334 1.359 -0.025 1.26e-02 6.30e+03 3.94e+00 ... (remaining 84100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 120497 2.82 - 5.63: 1643 5.63 - 8.45: 252 8.45 - 11.26: 46 11.26 - 14.08: 11 Bond angle restraints: 122449 Sorted by residual: angle pdb=" CA MET F 19 " pdb=" CB MET F 19 " pdb=" CG MET F 19 " ideal model delta sigma weight residual 114.10 125.03 -10.93 2.00e+00 2.50e-01 2.99e+01 angle pdb=" C2' C 21753 " pdb=" C1' C 21753 " pdb=" N1 C 21753 " ideal model delta sigma weight residual 112.00 120.12 -8.12 1.50e+00 4.44e-01 2.93e+01 angle pdb=" CA ARG Y 11 " pdb=" CB ARG Y 11 " pdb=" CG ARG Y 11 " ideal model delta sigma weight residual 114.10 124.58 -10.48 2.00e+00 2.50e-01 2.75e+01 angle pdb=" CA GLU J 132 " pdb=" CB GLU J 132 " pdb=" CG GLU J 132 " ideal model delta sigma weight residual 114.10 124.52 -10.42 2.00e+00 2.50e-01 2.71e+01 angle pdb=" C3' U 2 688 " pdb=" O3' U 2 688 " pdb=" P U 2 689 " ideal model delta sigma weight residual 120.20 127.95 -7.75 1.50e+00 4.44e-01 2.67e+01 ... (remaining 122444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 48478 35.98 - 71.96: 4600 71.96 - 107.94: 597 107.94 - 143.92: 16 143.92 - 179.90: 23 Dihedral angle restraints: 53714 sinusoidal: 39658 harmonic: 14056 Sorted by residual: 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 40.04 159.96 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U 2 823 " pdb=" C1' U 2 823 " pdb=" N1 U 2 823 " pdb=" C2 U 2 823 " ideal model delta sinusoidal sigma weight residual 200.00 42.03 157.97 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' C 21057 " pdb=" C1' C 21057 " pdb=" N1 C 21057 " pdb=" C2 C 21057 " ideal model delta sinusoidal sigma weight residual 200.00 42.89 157.11 1 1.50e+01 4.44e-03 8.20e+01 ... (remaining 53711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 14108 0.080 - 0.160: 983 0.160 - 0.239: 85 0.239 - 0.319: 15 0.319 - 0.399: 3 Chirality restraints: 15194 Sorted by residual: chirality pdb=" C1' C 21753 " pdb=" O4' C 21753 " pdb=" C2' C 21753 " pdb=" N1 C 21753 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB ILE M 56 " pdb=" CA ILE M 56 " pdb=" CG1 ILE M 56 " pdb=" CG2 ILE M 56 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3' U z 160 " pdb=" C4' U z 160 " pdb=" O3' U z 160 " pdb=" C2' U z 160 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 15191 not shown) Planarity restraints: 8634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 21753 " -0.048 2.00e-02 2.50e+03 3.20e-02 2.30e+01 pdb=" N1 C 21753 " 0.060 2.00e-02 2.50e+03 pdb=" C2 C 21753 " -0.042 2.00e-02 2.50e+03 pdb=" O2 C 21753 " 0.032 2.00e-02 2.50e+03 pdb=" N3 C 21753 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C 21753 " -0.013 2.00e-02 2.50e+03 pdb=" N4 C 21753 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C 21753 " 0.008 2.00e-02 2.50e+03 pdb=" C6 C 21753 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 596 " 0.028 2.00e-02 2.50e+03 1.99e-02 8.95e+00 pdb=" N1 U 2 596 " -0.046 2.00e-02 2.50e+03 pdb=" C2 U 2 596 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U 2 596 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U 2 596 " -0.012 2.00e-02 2.50e+03 pdb=" C4 U 2 596 " 0.020 2.00e-02 2.50e+03 pdb=" O4 U 2 596 " 0.000 2.00e-02 2.50e+03 pdb=" C5 U 2 596 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U 2 596 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21779 " 0.020 2.00e-02 2.50e+03 1.72e-02 8.91e+00 pdb=" N9 G 21779 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G 21779 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G 21779 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G 21779 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 21779 " 0.019 2.00e-02 2.50e+03 pdb=" O6 G 21779 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G 21779 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G 21779 " 0.035 2.00e-02 2.50e+03 pdb=" N2 G 21779 " -0.030 2.00e-02 2.50e+03 pdb=" N3 G 21779 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G 21779 " -0.002 2.00e-02 2.50e+03 ... (remaining 8631 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 14575 2.78 - 3.31: 64717 3.31 - 3.84: 148008 3.84 - 4.37: 167683 4.37 - 4.90: 249445 Nonbonded interactions: 644428 Sorted by model distance: nonbonded pdb=" O2' A 21332 " pdb=" O GLN E 145 " model vdw 2.245 3.040 nonbonded pdb=" OP1 U 21549 " pdb=" OH TYR e 34 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP O 56 " pdb=" OG1 THR c 52 " model vdw 2.270 3.040 nonbonded pdb=" O ASN B 164 " pdb=" OG SER B 170 " model vdw 2.271 3.040 nonbonded pdb=" O TYR L 57 " pdb=" OG1 THR L 72 " model vdw 2.272 3.040 ... (remaining 644423 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: 3.390 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: 0.120 Extract box with map and model: 2.370 Check model and map are aligned: 0.460 Set scattering table: 0.570 Process input model: 177.360 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 84105 Z= 0.212 Angle : 0.832 14.079 122449 Z= 0.410 Chirality : 0.042 0.399 15194 Planarity : 0.006 0.084 8634 Dihedral : 22.249 179.903 44648 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.11), residues: 4821 helix: -1.67 (0.11), residues: 1471 sheet: -1.05 (0.19), residues: 797 loop : -2.24 (0.11), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP K 7 HIS 0.016 0.001 HIS Q 54 PHE 0.049 0.002 PHE E 17 TYR 0.034 0.002 TYR S 84 ARG 0.021 0.001 ARG J 59 *********************** 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 815 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 815 time to evaluate : 4.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 PHE cc_start: 0.6819 (p90) cc_final: 0.5610 (p90) REVERT: B 37 TYR cc_start: 0.6470 (m-80) cc_final: 0.5457 (m-80) REVERT: C 110 MET cc_start: 0.7994 (tpt) cc_final: 0.7726 (tpp) REVERT: C 217 MET cc_start: 0.6734 (ttm) cc_final: 0.6243 (ttm) REVERT: D 190 SER cc_start: 0.6592 (t) cc_final: 0.6080 (m) REVERT: E 126 ILE cc_start: 0.8442 (pt) cc_final: 0.8191 (pt) REVERT: E 154 ASP cc_start: 0.5930 (p0) cc_final: 0.5241 (p0) REVERT: E 165 ASN cc_start: 0.7818 (m110) cc_final: 0.7522 (t0) REVERT: F 19 MET cc_start: 0.8253 (ttt) cc_final: 0.7939 (ttt) REVERT: F 40 GLU cc_start: 0.7869 (pm20) cc_final: 0.7650 (pm20) REVERT: F 123 LEU cc_start: 0.7575 (mt) cc_final: 0.7162 (mt) REVERT: G 172 CYS cc_start: 0.7662 (t) cc_final: 0.6946 (t) REVERT: G 176 GLU cc_start: 0.6692 (mp0) cc_final: 0.6226 (mp0) REVERT: G 194 ASP cc_start: 0.8219 (m-30) cc_final: 0.7776 (m-30) REVERT: H 181 THR cc_start: 0.8828 (m) cc_final: 0.8587 (p) REVERT: I 62 ILE cc_start: 0.7369 (mt) cc_final: 0.7125 (mt) REVERT: K 79 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6835 (mmm-85) REVERT: L 15 LEU cc_start: 0.7943 (tp) cc_final: 0.7581 (tp) REVERT: L 28 HIS cc_start: 0.7103 (m90) cc_final: 0.6862 (m90) REVERT: L 46 MET cc_start: 0.6657 (tmm) cc_final: 0.6443 (tmm) REVERT: L 69 TRP cc_start: 0.5624 (m-90) cc_final: 0.5326 (m-90) REVERT: L 71 LEU cc_start: 0.6652 (mt) cc_final: 0.5734 (tt) REVERT: M 109 MET cc_start: 0.8406 (ppp) cc_final: 0.7609 (ppp) REVERT: O 63 VAL cc_start: 0.8466 (t) cc_final: 0.8179 (p) REVERT: P 26 ASN cc_start: 0.7710 (m-40) cc_final: 0.7477 (m-40) REVERT: P 90 ILE cc_start: 0.6710 (mm) cc_final: 0.6331 (mt) REVERT: P 116 LEU cc_start: 0.8528 (mt) cc_final: 0.8109 (pp) REVERT: Q 89 MET cc_start: 0.6873 (ptt) cc_final: 0.6344 (ttp) REVERT: Q 106 GLU cc_start: 0.5563 (tm-30) cc_final: 0.5322 (tp30) REVERT: R 142 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7752 (mm-40) REVERT: S 24 LEU cc_start: 0.6656 (mm) cc_final: 0.6410 (mm) REVERT: S 58 MET cc_start: 0.6117 (mmp) cc_final: 0.5215 (ttp) REVERT: S 67 ARG cc_start: 0.4543 (tpt-90) cc_final: 0.4248 (tpt-90) REVERT: T 103 LEU cc_start: 0.7463 (mm) cc_final: 0.6817 (pp) REVERT: T 144 ARG cc_start: 0.3771 (ppt170) cc_final: 0.2978 (mmt180) REVERT: U 76 THR cc_start: 0.7645 (m) cc_final: 0.7266 (p) REVERT: U 112 MET cc_start: 0.7918 (mmm) cc_final: 0.7654 (tpp) REVERT: U 128 GLN cc_start: 0.7685 (pt0) cc_final: 0.6787 (tm-30) REVERT: V 62 ARG cc_start: 0.7249 (mmt90) cc_final: 0.7038 (mmt90) REVERT: W 12 TYR cc_start: 0.7750 (p90) cc_final: 0.7263 (p90) REVERT: W 15 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7130 (mtm-85) REVERT: X 91 ASN cc_start: 0.7866 (t0) cc_final: 0.7390 (t0) REVERT: a 76 ARG cc_start: 0.5596 (mmm160) cc_final: 0.5223 (mmt90) REVERT: e 40 ARG cc_start: 0.6654 (ptt-90) cc_final: 0.6372 (ptt-90) REVERT: f 88 GLN cc_start: 0.7889 (pm20) cc_final: 0.7637 (pm20) REVERT: h 79 LEU cc_start: 0.6054 (tp) cc_final: 0.5755 (tp) REVERT: h 129 ILE cc_start: 0.6549 (mm) cc_final: 0.6264 (mm) outliers start: 0 outliers final: 0 residues processed: 815 average time/residue: 0.7273 time to fit residues: 1025.5301 Evaluate side-chains 610 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 610 time to evaluate : 4.337 ------------------------------------------------------------------------------- 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: 10.0000 chunk 499 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 336 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 516 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 314 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 598 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS B 33 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN F 8 HIS F 209 HIS F 232 ASN H 227 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN L 66 HIS M 121 GLN N 48 HIS R 97 GLN ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 HIS S 74 GLN U 85 ASN U 126 GLN U 128 GLN W 82 ASN ** Y 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 HIS c 51 GLN e 3 HIS g 93 HIS h 188 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 84105 Z= 0.324 Angle : 0.741 11.081 122449 Z= 0.374 Chirality : 0.041 0.256 15194 Planarity : 0.006 0.076 8634 Dihedral : 23.737 179.431 34536 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.14 % Allowed : 7.52 % Favored : 92.34 % 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: -2.04 (0.11), residues: 4821 helix: -0.31 (0.13), residues: 1502 sheet: -1.21 (0.18), residues: 837 loop : -2.09 (0.11), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 64 HIS 0.014 0.002 HIS Q 54 PHE 0.030 0.002 PHE D 236 TYR 0.020 0.002 TYR G 188 ARG 0.015 0.001 ARG Y 11 *********************** 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 724 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 718 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.6711 (m-80) cc_final: 0.5333 (m-80) REVERT: C 110 MET cc_start: 0.8142 (tpt) cc_final: 0.7898 (tpp) REVERT: E 74 GLN cc_start: 0.7306 (tp-100) cc_final: 0.6792 (tp40) REVERT: E 162 ASP cc_start: 0.7554 (t0) cc_final: 0.6975 (t0) REVERT: E 165 ASN cc_start: 0.7673 (m110) cc_final: 0.7389 (m110) REVERT: F 42 LEU cc_start: 0.8269 (tt) cc_final: 0.7941 (tp) REVERT: F 45 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7887 (tp) REVERT: F 181 CYS cc_start: 0.6822 (p) cc_final: 0.6386 (p) REVERT: F 237 SER cc_start: 0.7435 (p) cc_final: 0.7201 (p) REVERT: G 88 MET cc_start: 0.6427 (ttm) cc_final: 0.5861 (ttm) REVERT: G 89 THR cc_start: 0.8200 (p) cc_final: 0.7648 (t) REVERT: G 172 CYS cc_start: 0.7793 (t) cc_final: 0.6952 (t) REVERT: G 176 GLU cc_start: 0.6906 (mp0) cc_final: 0.6463 (mp0) REVERT: H 21 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7149 (tm-30) REVERT: I 131 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7373 (tm-30) REVERT: J 132 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6825 (pp20) REVERT: L 15 LEU cc_start: 0.7889 (tp) cc_final: 0.7425 (tp) REVERT: L 53 LYS cc_start: 0.7833 (tptt) cc_final: 0.7561 (tptp) REVERT: L 71 LEU cc_start: 0.6717 (mt) cc_final: 0.5939 (tt) REVERT: M 12 LYS cc_start: 0.8452 (pptt) cc_final: 0.8248 (pptt) REVERT: M 103 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7181 (tm-30) REVERT: M 118 ARG cc_start: 0.5395 (tpp-160) cc_final: 0.5073 (tpp80) REVERT: O 142 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7362 (mp0) REVERT: P 90 ILE cc_start: 0.6717 (mm) cc_final: 0.6063 (tp) REVERT: P 116 LEU cc_start: 0.8556 (mt) cc_final: 0.8129 (pp) REVERT: P 130 GLU cc_start: 0.5766 (pm20) cc_final: 0.5225 (pm20) REVERT: P 138 ASP cc_start: 0.7279 (m-30) cc_final: 0.7033 (m-30) REVERT: Q 89 MET cc_start: 0.7020 (ptt) cc_final: 0.6660 (ttt) REVERT: Q 90 VAL cc_start: 0.5257 (t) cc_final: 0.4962 (p) REVERT: Q 94 VAL cc_start: 0.6438 (t) cc_final: 0.5940 (t) REVERT: R 16 LYS cc_start: 0.7442 (tmmt) cc_final: 0.7042 (tptp) REVERT: R 42 ILE cc_start: 0.6199 (mm) cc_final: 0.5940 (mm) REVERT: R 63 PHE cc_start: 0.7308 (m-80) cc_final: 0.6921 (m-80) REVERT: R 145 TYR cc_start: 0.4367 (m-80) cc_final: 0.3724 (m-80) REVERT: S 24 LEU cc_start: 0.7098 (mm) cc_final: 0.6810 (mm) REVERT: S 58 MET cc_start: 0.6859 (mmp) cc_final: 0.5996 (ttp) REVERT: S 96 ILE cc_start: 0.5888 (tp) cc_final: 0.5465 (tp) REVERT: T 58 GLU cc_start: 0.5651 (tp30) cc_final: 0.5030 (tp30) REVERT: T 103 LEU cc_start: 0.7662 (mm) cc_final: 0.7030 (pp) REVERT: U 128 GLN cc_start: 0.7749 (pt0) cc_final: 0.6762 (tm-30) REVERT: V 82 MET cc_start: 0.5579 (tpp) cc_final: 0.5104 (tpp) REVERT: W 12 TYR cc_start: 0.7910 (p90) cc_final: 0.7638 (p90) REVERT: W 82 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7831 (p0) REVERT: X 91 ASN cc_start: 0.7871 (t0) cc_final: 0.7359 (t0) REVERT: X 110 ILE cc_start: 0.8125 (mp) cc_final: 0.7924 (mp) REVERT: Y 9 THR cc_start: 0.8235 (p) cc_final: 0.7983 (p) REVERT: Y 19 ASP cc_start: 0.8522 (m-30) cc_final: 0.8219 (m-30) REVERT: a 76 ARG cc_start: 0.5842 (mmm160) cc_final: 0.5303 (mmt90) REVERT: c 33 MET cc_start: 0.6847 (mmm) cc_final: 0.5946 (mmm) REVERT: c 35 VAL cc_start: 0.8560 (t) cc_final: 0.8279 (p) REVERT: d 16 LYS cc_start: 0.4986 (tptm) cc_final: 0.4612 (mmmm) REVERT: e 34 TYR cc_start: 0.5384 (m-10) cc_final: 0.4986 (m-80) REVERT: f 109 MET cc_start: 0.6492 (tmm) cc_final: 0.6022 (tmm) REVERT: h 21 ILE cc_start: 0.5916 (mm) cc_final: 0.5683 (mm) REVERT: h 79 LEU cc_start: 0.5478 (tp) cc_final: 0.5005 (tp) REVERT: h 195 LEU cc_start: 0.7620 (mt) cc_final: 0.7358 (mm) REVERT: n 25 LYS cc_start: 0.4018 (mmpt) cc_final: 0.3815 (tttt) outliers start: 6 outliers final: 3 residues processed: 724 average time/residue: 0.7598 time to fit residues: 959.5177 Evaluate side-chains 572 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 567 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 332 optimal weight: 9.9990 chunk 185 optimal weight: 0.5980 chunk 498 optimal weight: 10.0000 chunk 407 optimal weight: 0.0770 chunk 165 optimal weight: 20.0000 chunk 599 optimal weight: 8.9990 chunk 647 optimal weight: 30.0000 chunk 533 optimal weight: 8.9990 chunk 594 optimal weight: 0.2980 chunk 204 optimal weight: 4.9990 chunk 480 optimal weight: 10.0000 overall best weight: 2.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 111 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN F 214 ASN G 95 HIS H 227 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS R 11 GLN R 97 GLN S 31 ASN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN U 42 HIS U 126 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 120 HIS Z 22 GLN e 41 GLN h 188 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 84105 Z= 0.166 Angle : 0.578 9.887 122449 Z= 0.295 Chirality : 0.036 0.234 15194 Planarity : 0.004 0.062 8634 Dihedral : 23.601 179.870 34536 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.83 % 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: -1.65 (0.12), residues: 4821 helix: 0.19 (0.13), residues: 1502 sheet: -1.08 (0.19), residues: 785 loop : -1.94 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP h 43 HIS 0.012 0.001 HIS G 95 PHE 0.024 0.001 PHE I 72 TYR 0.018 0.001 TYR S 84 ARG 0.011 0.000 ARG c 17 *********************** 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 761 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 759 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.6760 (m-80) cc_final: 0.5707 (m-80) REVERT: B 126 ASP cc_start: 0.7527 (t0) cc_final: 0.6925 (t70) REVERT: C 87 ILE cc_start: 0.8047 (tt) cc_final: 0.7637 (tt) REVERT: C 110 MET cc_start: 0.8149 (tpt) cc_final: 0.7800 (tpp) REVERT: C 217 MET cc_start: 0.6043 (ttt) cc_final: 0.5586 (ttm) REVERT: E 65 ARG cc_start: 0.5300 (mmm-85) cc_final: 0.4775 (tpp80) REVERT: E 69 LEU cc_start: 0.8080 (mm) cc_final: 0.7871 (mm) REVERT: E 74 GLN cc_start: 0.7257 (tp-100) cc_final: 0.6751 (tp40) REVERT: E 162 ASP cc_start: 0.7521 (t0) cc_final: 0.6945 (t0) REVERT: E 165 ASN cc_start: 0.7563 (m110) cc_final: 0.7202 (m-40) REVERT: F 19 MET cc_start: 0.8463 (ttt) cc_final: 0.8051 (ttt) REVERT: F 42 LEU cc_start: 0.8115 (tt) cc_final: 0.7830 (tp) REVERT: F 181 CYS cc_start: 0.6863 (p) cc_final: 0.6436 (p) REVERT: F 237 SER cc_start: 0.7135 (p) cc_final: 0.6823 (p) REVERT: G 88 MET cc_start: 0.6286 (ttm) cc_final: 0.5860 (ttm) REVERT: H 21 GLU cc_start: 0.7660 (tm-30) cc_final: 0.6973 (tm-30) REVERT: H 28 TYR cc_start: 0.5712 (m-80) cc_final: 0.5058 (m-80) REVERT: I 131 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7424 (tm-30) REVERT: J 80 ASP cc_start: 0.7609 (t0) cc_final: 0.7269 (m-30) REVERT: J 132 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6750 (pp20) REVERT: K 35 TYR cc_start: 0.7400 (m-80) cc_final: 0.6941 (m-10) REVERT: K 79 ARG cc_start: 0.7640 (mtm180) cc_final: 0.7346 (mmm-85) REVERT: L 53 LYS cc_start: 0.7807 (tptt) cc_final: 0.7530 (tptp) REVERT: L 71 LEU cc_start: 0.6779 (mt) cc_final: 0.5956 (tt) REVERT: M 118 ARG cc_start: 0.5404 (tpp-160) cc_final: 0.4814 (tpp80) REVERT: O 142 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7219 (mp0) REVERT: P 60 MET cc_start: 0.7048 (ptm) cc_final: 0.6743 (ptm) REVERT: P 90 ILE cc_start: 0.6636 (mm) cc_final: 0.6318 (mt) REVERT: P 116 LEU cc_start: 0.8511 (mt) cc_final: 0.8152 (pp) REVERT: P 131 ASP cc_start: 0.8162 (t0) cc_final: 0.7945 (t0) REVERT: P 138 ASP cc_start: 0.7174 (m-30) cc_final: 0.6875 (m-30) REVERT: Q 41 GLN cc_start: 0.7843 (mp10) cc_final: 0.7490 (mp10) REVERT: Q 89 MET cc_start: 0.7029 (ptt) cc_final: 0.6649 (ttt) REVERT: Q 90 VAL cc_start: 0.5158 (t) cc_final: 0.4882 (p) REVERT: Q 94 VAL cc_start: 0.6474 (t) cc_final: 0.5999 (t) REVERT: R 16 LYS cc_start: 0.7247 (tmmt) cc_final: 0.6881 (tmtt) REVERT: R 63 PHE cc_start: 0.7310 (m-80) cc_final: 0.6933 (m-80) REVERT: R 66 VAL cc_start: 0.7412 (m) cc_final: 0.6986 (m) REVERT: S 24 LEU cc_start: 0.7110 (mm) cc_final: 0.6854 (mm) REVERT: S 37 GLU cc_start: 0.6370 (pm20) cc_final: 0.6109 (pm20) REVERT: S 58 MET cc_start: 0.6816 (mmp) cc_final: 0.6071 (ttp) REVERT: S 67 ARG cc_start: 0.4324 (tpt-90) cc_final: 0.3982 (tpt-90) REVERT: S 96 ILE cc_start: 0.5818 (tp) cc_final: 0.5550 (tp) REVERT: T 58 GLU cc_start: 0.5764 (tp30) cc_final: 0.5455 (mm-30) REVERT: T 103 LEU cc_start: 0.7618 (mm) cc_final: 0.6984 (pp) REVERT: T 134 GLN cc_start: 0.7044 (mp10) cc_final: 0.6808 (mp10) REVERT: U 128 GLN cc_start: 0.7664 (pt0) cc_final: 0.6803 (tm-30) REVERT: V 82 MET cc_start: 0.5634 (tpp) cc_final: 0.5134 (tpp) REVERT: W 12 TYR cc_start: 0.7879 (p90) cc_final: 0.7602 (p90) REVERT: X 91 ASN cc_start: 0.7818 (t0) cc_final: 0.7323 (t0) REVERT: Y 19 ASP cc_start: 0.8368 (m-30) cc_final: 0.8132 (m-30) REVERT: a 76 ARG cc_start: 0.5844 (mmm160) cc_final: 0.5272 (mmt90) REVERT: c 33 MET cc_start: 0.6964 (mmm) cc_final: 0.6192 (mmm) REVERT: d 16 LYS cc_start: 0.4968 (tptm) cc_final: 0.4569 (mmmm) REVERT: d 54 ASP cc_start: 0.5792 (p0) cc_final: 0.5240 (t0) REVERT: d 67 ARG cc_start: 0.1136 (tpm170) cc_final: 0.0811 (tpp-160) REVERT: f 109 MET cc_start: 0.6563 (tmm) cc_final: 0.6096 (tmm) REVERT: h 21 ILE cc_start: 0.5817 (mm) cc_final: 0.5521 (mm) REVERT: h 79 LEU cc_start: 0.5547 (tp) cc_final: 0.5087 (tp) REVERT: h 129 ILE cc_start: 0.6355 (mm) cc_final: 0.6069 (mm) REVERT: h 195 LEU cc_start: 0.7305 (mt) cc_final: 0.7020 (mm) REVERT: h 302 TYR cc_start: 0.7492 (m-80) cc_final: 0.6704 (m-80) outliers start: 2 outliers final: 0 residues processed: 760 average time/residue: 0.8120 time to fit residues: 1073.8655 Evaluate side-chains 594 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 594 time to evaluate : 4.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 592 optimal weight: 8.9990 chunk 450 optimal weight: 0.5980 chunk 311 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 402 optimal weight: 6.9990 chunk 601 optimal weight: 6.9990 chunk 636 optimal weight: 30.0000 chunk 314 optimal weight: 10.0000 chunk 570 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN H 227 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS O 105 ASN P 83 GLN R 24 HIS R 97 GLN S 31 ASN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN T 42 HIS U 126 GLN U 128 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 84105 Z= 0.244 Angle : 0.664 11.239 122449 Z= 0.336 Chirality : 0.039 0.324 15194 Planarity : 0.005 0.070 8634 Dihedral : 23.663 179.911 34536 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.59 % 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: -1.63 (0.12), residues: 4821 helix: 0.25 (0.13), residues: 1499 sheet: -1.21 (0.19), residues: 770 loop : -1.90 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 7 HIS 0.012 0.002 HIS Q 54 PHE 0.029 0.002 PHE G 97 TYR 0.021 0.002 TYR C 133 ARG 0.010 0.001 ARG b 42 *********************** 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 734 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 730 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.6940 (m-80) cc_final: 0.6608 (m-80) REVERT: B 126 ASP cc_start: 0.7428 (t0) cc_final: 0.6810 (t70) REVERT: C 110 MET cc_start: 0.8194 (tpt) cc_final: 0.7942 (tpp) REVERT: C 217 MET cc_start: 0.6195 (ttt) cc_final: 0.5774 (ttm) REVERT: E 29 LEU cc_start: 0.6886 (mt) cc_final: 0.6604 (mt) REVERT: F 45 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7916 (tp) REVERT: F 181 CYS cc_start: 0.6623 (p) cc_final: 0.6259 (p) REVERT: F 198 ARG cc_start: 0.6887 (ttt180) cc_final: 0.6570 (tmm-80) REVERT: G 88 MET cc_start: 0.6374 (ttm) cc_final: 0.5873 (ttm) REVERT: G 89 THR cc_start: 0.8123 (p) cc_final: 0.7536 (t) REVERT: H 28 TYR cc_start: 0.5815 (m-80) cc_final: 0.5549 (m-80) REVERT: H 63 MET cc_start: 0.6802 (tpt) cc_final: 0.6469 (tpt) REVERT: H 218 LYS cc_start: 0.4566 (tmmt) cc_final: 0.4271 (tttp) REVERT: H 219 GLU cc_start: 0.4196 (mt-10) cc_final: 0.3963 (mm-30) REVERT: I 30 LEU cc_start: 0.7690 (tp) cc_final: 0.7143 (tp) REVERT: I 131 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7353 (tm-30) REVERT: J 80 ASP cc_start: 0.7641 (t0) cc_final: 0.7298 (m-30) REVERT: K 79 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7325 (mmm-85) REVERT: L 53 LYS cc_start: 0.7843 (tptt) cc_final: 0.7553 (tptp) REVERT: L 69 TRP cc_start: 0.5905 (m-90) cc_final: 0.5603 (m-90) REVERT: L 71 LEU cc_start: 0.6922 (mt) cc_final: 0.6195 (tt) REVERT: M 118 ARG cc_start: 0.5275 (tpp-160) cc_final: 0.4778 (tpp80) REVERT: O 142 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7266 (mp0) REVERT: P 60 MET cc_start: 0.6821 (ptm) cc_final: 0.6460 (ptm) REVERT: P 90 ILE cc_start: 0.6645 (mm) cc_final: 0.6334 (mt) REVERT: P 116 LEU cc_start: 0.8527 (mt) cc_final: 0.8123 (pp) REVERT: P 130 GLU cc_start: 0.5522 (pm20) cc_final: 0.5121 (pm20) REVERT: Q 34 MET cc_start: 0.7560 (mmm) cc_final: 0.7182 (mmm) REVERT: Q 41 GLN cc_start: 0.7861 (mp10) cc_final: 0.7436 (mp10) REVERT: Q 89 MET cc_start: 0.7003 (ptt) cc_final: 0.6455 (ttt) REVERT: Q 90 VAL cc_start: 0.5358 (t) cc_final: 0.5085 (p) REVERT: R 16 LYS cc_start: 0.7452 (tmmt) cc_final: 0.7077 (tmtt) REVERT: R 41 MET cc_start: 0.4980 (mtt) cc_final: 0.4541 (mtt) REVERT: R 66 VAL cc_start: 0.7596 (m) cc_final: 0.6984 (m) REVERT: R 123 ASP cc_start: 0.6929 (t0) cc_final: 0.6621 (t0) REVERT: S 24 LEU cc_start: 0.7190 (mm) cc_final: 0.6741 (mm) REVERT: S 37 GLU cc_start: 0.6439 (pm20) cc_final: 0.6223 (pm20) REVERT: S 58 MET cc_start: 0.7248 (mmp) cc_final: 0.6486 (ttp) REVERT: T 58 GLU cc_start: 0.5663 (tp30) cc_final: 0.5156 (tp30) REVERT: T 103 LEU cc_start: 0.7625 (mm) cc_final: 0.6945 (pp) REVERT: T 134 GLN cc_start: 0.6992 (mp10) cc_final: 0.6625 (mp10) REVERT: U 128 GLN cc_start: 0.7773 (pt0) cc_final: 0.6806 (tm-30) REVERT: V 82 MET cc_start: 0.5434 (tpp) cc_final: 0.4977 (tpp) REVERT: W 12 TYR cc_start: 0.7938 (p90) cc_final: 0.7722 (p90) REVERT: X 91 ASN cc_start: 0.7921 (t0) cc_final: 0.7461 (t0) REVERT: Y 23 HIS cc_start: 0.6546 (t-170) cc_final: 0.6342 (t-90) REVERT: a 76 ARG cc_start: 0.5825 (mmm160) cc_final: 0.5333 (mmt90) REVERT: c 13 GLU cc_start: 0.6795 (pm20) cc_final: 0.6584 (pm20) REVERT: c 33 MET cc_start: 0.7141 (mmm) cc_final: 0.6307 (mmm) REVERT: d 16 LYS cc_start: 0.5041 (tptm) cc_final: 0.4585 (mmmm) REVERT: d 54 ASP cc_start: 0.6105 (p0) cc_final: 0.5400 (t0) REVERT: e 34 TYR cc_start: 0.5139 (m-10) cc_final: 0.4918 (m-80) REVERT: f 109 MET cc_start: 0.6277 (tmm) cc_final: 0.5549 (tmm) REVERT: h 21 ILE cc_start: 0.5762 (mm) cc_final: 0.5527 (mm) REVERT: h 79 LEU cc_start: 0.5477 (tp) cc_final: 0.4956 (tp) REVERT: h 129 ILE cc_start: 0.6539 (mm) cc_final: 0.6235 (mm) REVERT: h 149 GLU cc_start: 0.8240 (pp20) cc_final: 0.7490 (pp20) outliers start: 4 outliers final: 1 residues processed: 734 average time/residue: 0.7335 time to fit residues: 933.1519 Evaluate side-chains 585 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 583 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 530 optimal weight: 9.9990 chunk 361 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 474 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 543 optimal weight: 0.0980 chunk 440 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 325 optimal weight: 6.9990 chunk 571 optimal weight: 3.9990 chunk 160 optimal weight: 30.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN F 232 ASN H 227 GLN J 9 HIS ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS S 31 ASN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 125 HIS ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN V 81 GLN W 33 GLN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 84105 Z= 0.255 Angle : 0.665 10.759 122449 Z= 0.337 Chirality : 0.039 0.265 15194 Planarity : 0.005 0.058 8634 Dihedral : 23.700 179.506 34536 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.05 % Allowed : 4.34 % Favored : 95.61 % 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: -1.66 (0.12), residues: 4821 helix: 0.26 (0.13), residues: 1502 sheet: -1.34 (0.19), residues: 755 loop : -1.91 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 7 HIS 0.010 0.001 HIS Q 54 PHE 0.025 0.002 PHE I 135 TYR 0.027 0.002 TYR E 167 ARG 0.015 0.001 ARG W 61 *********************** 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 731 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 729 time to evaluate : 4.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.7078 (m-80) cc_final: 0.6573 (m-80) REVERT: B 84 GLN cc_start: 0.8506 (mt0) cc_final: 0.8269 (mt0) REVERT: B 126 ASP cc_start: 0.7341 (t0) cc_final: 0.6703 (t70) REVERT: C 110 MET cc_start: 0.8292 (tpt) cc_final: 0.7935 (tpp) REVERT: C 122 GLU cc_start: 0.6572 (mp0) cc_final: 0.6296 (mp0) REVERT: C 217 MET cc_start: 0.6302 (ttt) cc_final: 0.6045 (ttt) REVERT: E 65 ARG cc_start: 0.5409 (tpt-90) cc_final: 0.5034 (tpt-90) REVERT: F 19 MET cc_start: 0.8348 (ttt) cc_final: 0.8137 (ttt) REVERT: F 181 CYS cc_start: 0.6613 (p) cc_final: 0.6211 (p) REVERT: G 88 MET cc_start: 0.6517 (ttm) cc_final: 0.6023 (ttm) REVERT: G 89 THR cc_start: 0.7995 (p) cc_final: 0.7521 (t) REVERT: G 176 GLU cc_start: 0.6734 (mp0) cc_final: 0.6483 (mp0) REVERT: H 28 TYR cc_start: 0.5825 (m-80) cc_final: 0.5507 (m-80) REVERT: H 156 TYR cc_start: 0.7517 (m-80) cc_final: 0.7070 (m-80) REVERT: H 218 LYS cc_start: 0.4662 (tmmt) cc_final: 0.4230 (ptmm) REVERT: I 131 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7331 (tm-30) REVERT: J 80 ASP cc_start: 0.7634 (t0) cc_final: 0.7309 (m-30) REVERT: K 79 ARG cc_start: 0.7545 (mtm180) cc_final: 0.7175 (mmm-85) REVERT: L 53 LYS cc_start: 0.7851 (tptt) cc_final: 0.7583 (tptp) REVERT: L 71 LEU cc_start: 0.7025 (mt) cc_final: 0.6065 (tt) REVERT: O 128 TYR cc_start: 0.8249 (t80) cc_final: 0.8026 (t80) REVERT: O 142 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7318 (mp0) REVERT: P 60 MET cc_start: 0.6720 (ptm) cc_final: 0.6376 (ptm) REVERT: P 90 ILE cc_start: 0.6551 (mm) cc_final: 0.6029 (tp) REVERT: P 116 LEU cc_start: 0.8571 (mt) cc_final: 0.8118 (pp) REVERT: Q 41 GLN cc_start: 0.7861 (mp10) cc_final: 0.7432 (mp10) REVERT: Q 89 MET cc_start: 0.6977 (ptt) cc_final: 0.6398 (ttt) REVERT: Q 90 VAL cc_start: 0.5425 (t) cc_final: 0.5189 (p) REVERT: Q 94 VAL cc_start: 0.6183 (t) cc_final: 0.5778 (t) REVERT: R 16 LYS cc_start: 0.7384 (tmmt) cc_final: 0.6942 (tmtt) REVERT: R 66 VAL cc_start: 0.7524 (m) cc_final: 0.6902 (m) REVERT: R 123 ASP cc_start: 0.6937 (t0) cc_final: 0.6681 (t0) REVERT: S 24 LEU cc_start: 0.7456 (mm) cc_final: 0.7033 (mm) REVERT: S 30 THR cc_start: 0.7857 (t) cc_final: 0.7607 (t) REVERT: S 58 MET cc_start: 0.7414 (mmp) cc_final: 0.6419 (ttp) REVERT: T 58 GLU cc_start: 0.5592 (tp30) cc_final: 0.5129 (tp30) REVERT: T 60 THR cc_start: 0.6214 (p) cc_final: 0.5540 (p) REVERT: T 103 LEU cc_start: 0.7598 (mm) cc_final: 0.6904 (pp) REVERT: T 134 GLN cc_start: 0.6974 (mp10) cc_final: 0.6714 (mp10) REVERT: U 128 GLN cc_start: 0.7714 (pt0) cc_final: 0.6921 (tm-30) REVERT: V 82 MET cc_start: 0.5573 (tpp) cc_final: 0.5061 (tpp) REVERT: W 12 TYR cc_start: 0.7906 (p90) cc_final: 0.7657 (p90) REVERT: X 91 ASN cc_start: 0.7907 (t0) cc_final: 0.7469 (t0) REVERT: Y 23 HIS cc_start: 0.6470 (t-170) cc_final: 0.6253 (t-170) REVERT: Z 101 LYS cc_start: 0.7564 (pttt) cc_final: 0.7113 (ptmm) REVERT: a 76 ARG cc_start: 0.5867 (mmm160) cc_final: 0.5324 (mmt90) REVERT: a 106 GLN cc_start: 0.6454 (pp30) cc_final: 0.5237 (pp30) REVERT: a 111 ARG cc_start: 0.3672 (ptp90) cc_final: 0.3276 (ttp-110) REVERT: c 33 MET cc_start: 0.7177 (mmm) cc_final: 0.6481 (mmm) REVERT: d 16 LYS cc_start: 0.5179 (tptm) cc_final: 0.4661 (mmmm) REVERT: d 54 ASP cc_start: 0.6290 (p0) cc_final: 0.5591 (t0) REVERT: e 34 TYR cc_start: 0.5242 (m-10) cc_final: 0.4990 (m-80) REVERT: f 109 MET cc_start: 0.6266 (tmm) cc_final: 0.5680 (tmm) REVERT: h 21 ILE cc_start: 0.5754 (mm) cc_final: 0.5503 (mm) REVERT: h 79 LEU cc_start: 0.5778 (tp) cc_final: 0.5101 (tp) REVERT: h 111 VAL cc_start: 0.7311 (m) cc_final: 0.7072 (m) REVERT: h 129 ILE cc_start: 0.6494 (mm) cc_final: 0.6201 (mm) outliers start: 2 outliers final: 0 residues processed: 731 average time/residue: 0.7166 time to fit residues: 907.1739 Evaluate side-chains 587 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 587 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 214 optimal weight: 0.4980 chunk 573 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 373 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 637 optimal weight: 0.5980 chunk 529 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN F 209 HIS F 232 ASN H 227 GLN I 33 ASN I 114 GLN L 44 HIS N 55 ASN S 31 ASN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN U 128 GLN ** f 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 14 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3249 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= 0.209 Angle : 0.623 9.956 122449 Z= 0.317 Chirality : 0.038 0.258 15194 Planarity : 0.005 0.051 8634 Dihedral : 23.649 179.840 34536 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % 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: -1.62 (0.12), residues: 4821 helix: 0.33 (0.13), residues: 1507 sheet: -1.37 (0.19), residues: 730 loop : -1.88 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 7 HIS 0.009 0.001 HIS G 95 PHE 0.026 0.002 PHE E 17 TYR 0.026 0.002 TYR N 61 ARG 0.013 0.001 ARG W 61 *********************** 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 715 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 712 time to evaluate : 4.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 ASP cc_start: 0.7301 (t0) cc_final: 0.6554 (t70) REVERT: C 110 MET cc_start: 0.8296 (tpt) cc_final: 0.7946 (tpp) REVERT: C 217 MET cc_start: 0.6245 (ttt) cc_final: 0.5728 (ttm) REVERT: E 65 ARG cc_start: 0.5382 (tpt-90) cc_final: 0.4928 (tpt-90) REVERT: E 210 ILE cc_start: 0.7769 (mp) cc_final: 0.7472 (tt) REVERT: F 154 ILE cc_start: 0.6461 (mm) cc_final: 0.6240 (mm) REVERT: F 181 CYS cc_start: 0.6624 (p) cc_final: 0.6237 (p) REVERT: G 88 MET cc_start: 0.6414 (ttm) cc_final: 0.6006 (ttm) REVERT: G 176 GLU cc_start: 0.6777 (mp0) cc_final: 0.6558 (mp0) REVERT: H 28 TYR cc_start: 0.5910 (m-80) cc_final: 0.5575 (m-80) REVERT: H 156 TYR cc_start: 0.7513 (m-80) cc_final: 0.7105 (m-80) REVERT: H 218 LYS cc_start: 0.4686 (tmmt) cc_final: 0.4214 (ptmm) REVERT: I 131 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7315 (tm-30) REVERT: I 172 THR cc_start: 0.7500 (p) cc_final: 0.7247 (t) REVERT: J 80 ASP cc_start: 0.7624 (t0) cc_final: 0.7280 (m-30) REVERT: J 132 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6681 (pp20) REVERT: K 79 ARG cc_start: 0.7574 (mtm180) cc_final: 0.7342 (mmm-85) REVERT: L 53 LYS cc_start: 0.7840 (tptt) cc_final: 0.7575 (tptp) REVERT: L 69 TRP cc_start: 0.6121 (m-90) cc_final: 0.5797 (m-90) REVERT: L 71 LEU cc_start: 0.6881 (mt) cc_final: 0.5820 (tt) REVERT: M 12 LYS cc_start: 0.8607 (pptt) cc_final: 0.8276 (pptt) REVERT: M 118 ARG cc_start: 0.5265 (tpp-160) cc_final: 0.4803 (tpp80) REVERT: O 142 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7163 (mp0) REVERT: P 60 MET cc_start: 0.6756 (ptm) cc_final: 0.6420 (ptm) REVERT: P 90 ILE cc_start: 0.6685 (mm) cc_final: 0.6344 (mt) REVERT: P 116 LEU cc_start: 0.8612 (mt) cc_final: 0.8226 (pp) REVERT: P 130 GLU cc_start: 0.5492 (pm20) cc_final: 0.5068 (pm20) REVERT: Q 34 MET cc_start: 0.7745 (mmm) cc_final: 0.7388 (mmm) REVERT: Q 37 TYR cc_start: 0.5969 (p90) cc_final: 0.5756 (p90) REVERT: Q 41 GLN cc_start: 0.7833 (mp10) cc_final: 0.7410 (mp10) REVERT: Q 89 MET cc_start: 0.6947 (ptt) cc_final: 0.6302 (ttt) REVERT: Q 90 VAL cc_start: 0.5238 (t) cc_final: 0.4989 (p) REVERT: Q 94 VAL cc_start: 0.6179 (t) cc_final: 0.5797 (t) REVERT: R 16 LYS cc_start: 0.7488 (tmmt) cc_final: 0.7026 (tmtt) REVERT: R 116 ASP cc_start: 0.6465 (m-30) cc_final: 0.6257 (p0) REVERT: R 123 ASP cc_start: 0.7042 (t0) cc_final: 0.6786 (t0) REVERT: S 24 LEU cc_start: 0.7398 (mm) cc_final: 0.7011 (mm) REVERT: S 58 MET cc_start: 0.7323 (mmp) cc_final: 0.6370 (ttp) REVERT: S 67 ARG cc_start: 0.4338 (tpt-90) cc_final: 0.4115 (tpt-90) REVERT: S 96 ILE cc_start: 0.5862 (tp) cc_final: 0.5600 (tp) REVERT: T 58 GLU cc_start: 0.5418 (tp30) cc_final: 0.5043 (tp30) REVERT: T 103 LEU cc_start: 0.7486 (mm) cc_final: 0.6860 (pp) REVERT: T 134 GLN cc_start: 0.6983 (mp10) cc_final: 0.6733 (mp10) REVERT: U 112 MET cc_start: 0.7488 (mmm) cc_final: 0.6981 (tpp) REVERT: U 128 GLN cc_start: 0.7714 (pt0) cc_final: 0.6773 (tm-30) REVERT: V 82 MET cc_start: 0.5573 (tpp) cc_final: 0.5030 (tpp) REVERT: W 12 TYR cc_start: 0.7895 (p90) cc_final: 0.7599 (p90) REVERT: W 61 ARG cc_start: 0.6554 (ttt180) cc_final: 0.5882 (ttm110) REVERT: W 69 ILE cc_start: 0.7907 (tp) cc_final: 0.7636 (tt) REVERT: X 91 ASN cc_start: 0.7872 (t0) cc_final: 0.7401 (t0) REVERT: Y 23 HIS cc_start: 0.6451 (t-170) cc_final: 0.6112 (t-90) REVERT: a 76 ARG cc_start: 0.5627 (mmm160) cc_final: 0.5263 (mmt90) REVERT: a 111 ARG cc_start: 0.3638 (ptp90) cc_final: 0.3242 (ttm110) REVERT: c 33 MET cc_start: 0.7288 (mmm) cc_final: 0.6537 (mmm) REVERT: d 16 LYS cc_start: 0.5203 (tptm) cc_final: 0.4699 (mmmm) REVERT: d 54 ASP cc_start: 0.6204 (p0) cc_final: 0.5561 (t0) REVERT: e 34 TYR cc_start: 0.5252 (m-10) cc_final: 0.5026 (m-80) REVERT: f 109 MET cc_start: 0.6264 (tmm) cc_final: 0.5691 (tmm) REVERT: g 132 MET cc_start: 0.1631 (tmm) cc_final: 0.0040 (mmt) REVERT: h 21 ILE cc_start: 0.5607 (mm) cc_final: 0.5279 (mm) REVERT: h 79 LEU cc_start: 0.5612 (tp) cc_final: 0.4958 (tp) REVERT: h 129 ILE cc_start: 0.6525 (mm) cc_final: 0.6216 (mm) REVERT: h 149 GLU cc_start: 0.8389 (pp20) cc_final: 0.7300 (pp20) REVERT: h 302 TYR cc_start: 0.7447 (m-80) cc_final: 0.6087 (m-80) outliers start: 3 outliers final: 0 residues processed: 715 average time/residue: 0.7187 time to fit residues: 892.6804 Evaluate side-chains 582 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 614 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 363 optimal weight: 5.9990 chunk 465 optimal weight: 8.9990 chunk 360 optimal weight: 10.0000 chunk 536 optimal weight: 0.8980 chunk 356 optimal weight: 5.9990 chunk 635 optimal weight: 10.0000 chunk 397 optimal weight: 9.9990 chunk 387 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN C 101 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN H 227 GLN ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS R 97 GLN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 GLN ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN f 117 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 84105 Z= 0.264 Angle : 0.685 9.862 122449 Z= 0.347 Chirality : 0.040 0.267 15194 Planarity : 0.005 0.065 8634 Dihedral : 23.746 178.653 34536 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % 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: -1.77 (0.12), residues: 4821 helix: 0.25 (0.13), residues: 1493 sheet: -1.46 (0.18), residues: 756 loop : -2.00 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP h 43 HIS 0.012 0.001 HIS Q 54 PHE 0.025 0.002 PHE I 135 TYR 0.041 0.002 TYR E 167 ARG 0.015 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 712 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 710 time to evaluate : 4.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 ASP cc_start: 0.7174 (t0) cc_final: 0.6606 (t70) REVERT: B 156 TYR cc_start: 0.7977 (m-10) cc_final: 0.7758 (m-10) REVERT: C 110 MET cc_start: 0.8376 (tpt) cc_final: 0.7859 (tpp) REVERT: C 217 MET cc_start: 0.6127 (ttt) cc_final: 0.5796 (ttt) REVERT: D 113 GLN cc_start: 0.6343 (mt0) cc_final: 0.4979 (mm-40) REVERT: E 17 PHE cc_start: 0.7298 (t80) cc_final: 0.6992 (t80) REVERT: E 65 ARG cc_start: 0.5378 (tpt-90) cc_final: 0.4545 (tpp80) REVERT: E 69 LEU cc_start: 0.8135 (mm) cc_final: 0.7815 (mm) REVERT: E 210 ILE cc_start: 0.7570 (mp) cc_final: 0.7366 (tt) REVERT: F 181 CYS cc_start: 0.6552 (p) cc_final: 0.6165 (p) REVERT: G 89 THR cc_start: 0.8124 (p) cc_final: 0.7660 (t) REVERT: H 28 TYR cc_start: 0.5936 (m-80) cc_final: 0.5647 (m-80) REVERT: H 156 TYR cc_start: 0.7543 (m-80) cc_final: 0.6988 (m-80) REVERT: H 218 LYS cc_start: 0.4458 (tmmt) cc_final: 0.4205 (ptmm) REVERT: I 131 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7284 (tm-30) REVERT: J 80 ASP cc_start: 0.7614 (t0) cc_final: 0.7251 (m-30) REVERT: L 14 LEU cc_start: 0.8263 (tp) cc_final: 0.8000 (tp) REVERT: L 49 MET cc_start: 0.4335 (tpt) cc_final: 0.4004 (tpt) REVERT: L 53 LYS cc_start: 0.7838 (tptt) cc_final: 0.7574 (tptp) REVERT: L 71 LEU cc_start: 0.6919 (mt) cc_final: 0.5926 (tt) REVERT: O 142 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7196 (mp0) REVERT: P 60 MET cc_start: 0.6717 (ptm) cc_final: 0.6419 (ptm) REVERT: P 90 ILE cc_start: 0.6443 (mm) cc_final: 0.5924 (tp) REVERT: P 116 LEU cc_start: 0.8666 (mt) cc_final: 0.8204 (pp) REVERT: P 130 GLU cc_start: 0.5495 (pm20) cc_final: 0.5031 (pm20) REVERT: Q 41 GLN cc_start: 0.7833 (mp10) cc_final: 0.7372 (mp10) REVERT: Q 89 MET cc_start: 0.6965 (ptt) cc_final: 0.6047 (ttp) REVERT: Q 90 VAL cc_start: 0.5421 (t) cc_final: 0.5181 (p) REVERT: Q 94 VAL cc_start: 0.5949 (t) cc_final: 0.5699 (t) REVERT: R 16 LYS cc_start: 0.7634 (tmmt) cc_final: 0.7191 (tmtt) REVERT: R 123 ASP cc_start: 0.6954 (t0) cc_final: 0.6591 (t0) REVERT: S 24 LEU cc_start: 0.7462 (mm) cc_final: 0.7133 (mm) REVERT: S 58 MET cc_start: 0.7349 (mmp) cc_final: 0.6431 (ttp) REVERT: S 67 ARG cc_start: 0.4474 (tpt-90) cc_final: 0.4232 (tpt-90) REVERT: T 58 GLU cc_start: 0.5401 (tp30) cc_final: 0.5083 (tp30) REVERT: T 83 PHE cc_start: 0.6033 (t80) cc_final: 0.5478 (t80) REVERT: T 103 LEU cc_start: 0.7522 (mm) cc_final: 0.6903 (pp) REVERT: T 134 GLN cc_start: 0.6946 (mp10) cc_final: 0.6634 (mp10) REVERT: U 128 GLN cc_start: 0.7712 (pt0) cc_final: 0.6881 (tm-30) REVERT: V 81 GLN cc_start: 0.6699 (tt0) cc_final: 0.6281 (tt0) REVERT: V 82 MET cc_start: 0.5560 (tpp) cc_final: 0.5237 (tpp) REVERT: W 12 TYR cc_start: 0.7885 (p90) cc_final: 0.7597 (p90) REVERT: W 61 ARG cc_start: 0.6656 (ttt180) cc_final: 0.6306 (ttm110) REVERT: W 69 ILE cc_start: 0.7987 (tp) cc_final: 0.7679 (tt) REVERT: X 91 ASN cc_start: 0.7931 (t0) cc_final: 0.7461 (t0) REVERT: Y 23 HIS cc_start: 0.6525 (t-170) cc_final: 0.6236 (t-170) REVERT: Z 101 LYS cc_start: 0.7542 (pttt) cc_final: 0.7114 (ptmm) REVERT: a 76 ARG cc_start: 0.5570 (mmm160) cc_final: 0.5306 (mmt90) REVERT: a 111 ARG cc_start: 0.3855 (ptp90) cc_final: 0.3457 (ttp-110) REVERT: c 33 MET cc_start: 0.7280 (mmm) cc_final: 0.6583 (mmm) REVERT: d 16 LYS cc_start: 0.5278 (tptm) cc_final: 0.4775 (mmmm) REVERT: d 29 GLN cc_start: 0.5997 (pp30) cc_final: 0.5738 (pp30) REVERT: f 109 MET cc_start: 0.6298 (tmm) cc_final: 0.5699 (tmm) REVERT: h 21 ILE cc_start: 0.5580 (mm) cc_final: 0.5246 (mm) REVERT: h 79 LEU cc_start: 0.5898 (tp) cc_final: 0.5259 (tp) REVERT: h 129 ILE cc_start: 0.6537 (mm) cc_final: 0.6290 (mm) outliers start: 2 outliers final: 1 residues processed: 712 average time/residue: 0.7272 time to fit residues: 903.0343 Evaluate side-chains 585 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 584 time to evaluate : 4.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 392 optimal weight: 4.9990 chunk 253 optimal weight: 0.0050 chunk 379 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 403 optimal weight: 6.9990 chunk 432 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 499 optimal weight: 9.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN H 227 GLN L 44 HIS M 106 HIS S 31 ASN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 GLN ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 125 HIS ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN ** b 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 84105 Z= 0.218 Angle : 0.640 9.977 122449 Z= 0.325 Chirality : 0.038 0.293 15194 Planarity : 0.005 0.060 8634 Dihedral : 23.697 179.670 34536 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.02 % Allowed : 1.33 % Favored : 98.65 % 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: -1.68 (0.12), residues: 4821 helix: 0.35 (0.13), residues: 1495 sheet: -1.44 (0.19), residues: 755 loop : -1.96 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP h 43 HIS 0.009 0.001 HIS Q 54 PHE 0.024 0.002 PHE C 25 TYR 0.028 0.002 TYR G 56 ARG 0.008 0.001 ARG D 194 *********************** 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 715 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 714 time to evaluate : 4.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 MET cc_start: 0.7964 (mtt) cc_final: 0.7723 (mtt) REVERT: B 126 ASP cc_start: 0.7105 (t0) cc_final: 0.6641 (t70) REVERT: C 87 ILE cc_start: 0.8135 (tt) cc_final: 0.7777 (tt) REVERT: C 110 MET cc_start: 0.8334 (tpt) cc_final: 0.7895 (tpp) REVERT: C 217 MET cc_start: 0.6113 (ttt) cc_final: 0.5586 (ttm) REVERT: D 68 ARG cc_start: 0.7992 (tpt170) cc_final: 0.7550 (tpt90) REVERT: D 113 GLN cc_start: 0.6526 (mt0) cc_final: 0.5083 (mm-40) REVERT: E 65 ARG cc_start: 0.5389 (tpt-90) cc_final: 0.4683 (tpp80) REVERT: E 210 ILE cc_start: 0.7778 (mp) cc_final: 0.7465 (tt) REVERT: F 181 CYS cc_start: 0.6577 (p) cc_final: 0.6248 (p) REVERT: F 237 SER cc_start: 0.7230 (p) cc_final: 0.6826 (p) REVERT: G 89 THR cc_start: 0.7991 (p) cc_final: 0.7366 (t) REVERT: H 1 MET cc_start: 0.7331 (tpp) cc_final: 0.6959 (mmm) REVERT: H 28 TYR cc_start: 0.5932 (m-80) cc_final: 0.5621 (m-80) REVERT: H 63 MET cc_start: 0.6682 (tpt) cc_final: 0.6467 (tpt) REVERT: H 156 TYR cc_start: 0.7272 (m-80) cc_final: 0.6909 (m-80) REVERT: H 218 LYS cc_start: 0.4375 (tmmt) cc_final: 0.4121 (ptmm) REVERT: I 97 GLN cc_start: 0.6666 (mm110) cc_final: 0.6362 (mm110) REVERT: I 131 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7297 (tm-30) REVERT: J 80 ASP cc_start: 0.7571 (t0) cc_final: 0.7216 (m-30) REVERT: L 53 LYS cc_start: 0.7853 (tptt) cc_final: 0.7592 (tptp) REVERT: L 69 TRP cc_start: 0.6083 (m-90) cc_final: 0.5737 (m-90) REVERT: L 71 LEU cc_start: 0.6940 (mt) cc_final: 0.5915 (tt) REVERT: M 118 ARG cc_start: 0.5248 (tpp-160) cc_final: 0.4817 (tpp80) REVERT: O 128 TYR cc_start: 0.8344 (t80) cc_final: 0.8075 (t80) REVERT: O 142 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7171 (mp0) REVERT: P 60 MET cc_start: 0.6708 (ptm) cc_final: 0.6404 (ptm) REVERT: P 90 ILE cc_start: 0.6694 (mm) cc_final: 0.6346 (mt) REVERT: P 116 LEU cc_start: 0.8668 (mt) cc_final: 0.8219 (pp) REVERT: Q 37 TYR cc_start: 0.6010 (p90) cc_final: 0.5742 (p90) REVERT: Q 41 GLN cc_start: 0.7826 (mp10) cc_final: 0.7415 (mp10) REVERT: Q 89 MET cc_start: 0.6958 (ptt) cc_final: 0.6040 (ttp) REVERT: Q 90 VAL cc_start: 0.5429 (t) cc_final: 0.5200 (p) REVERT: Q 94 VAL cc_start: 0.5866 (t) cc_final: 0.5585 (t) REVERT: Q 119 PHE cc_start: 0.5443 (m-10) cc_final: 0.4673 (m-80) REVERT: R 16 LYS cc_start: 0.7549 (tmmt) cc_final: 0.7098 (tmtt) REVERT: R 42 ILE cc_start: 0.6719 (mm) cc_final: 0.6493 (mm) REVERT: R 123 ASP cc_start: 0.7040 (t0) cc_final: 0.6737 (t0) REVERT: S 24 LEU cc_start: 0.7485 (mm) cc_final: 0.7057 (mm) REVERT: S 58 MET cc_start: 0.7306 (mmp) cc_final: 0.6363 (ttp) REVERT: S 96 ILE cc_start: 0.6203 (tp) cc_final: 0.5778 (tp) REVERT: T 58 GLU cc_start: 0.5447 (tp30) cc_final: 0.5126 (tp30) REVERT: T 83 PHE cc_start: 0.5906 (t80) cc_final: 0.5470 (t80) REVERT: T 103 LEU cc_start: 0.7451 (mm) cc_final: 0.6919 (pp) REVERT: T 134 GLN cc_start: 0.7023 (mp10) cc_final: 0.6739 (mp10) REVERT: U 128 GLN cc_start: 0.7769 (pt0) cc_final: 0.6947 (tm-30) REVERT: V 82 MET cc_start: 0.5754 (tpp) cc_final: 0.5144 (tpp) REVERT: W 12 TYR cc_start: 0.7880 (p90) cc_final: 0.7556 (p90) REVERT: W 69 ILE cc_start: 0.7940 (tp) cc_final: 0.7619 (tt) REVERT: X 34 ILE cc_start: 0.9313 (tp) cc_final: 0.9057 (tp) REVERT: X 91 ASN cc_start: 0.7868 (t0) cc_final: 0.7434 (t0) REVERT: Y 23 HIS cc_start: 0.6457 (t-170) cc_final: 0.6224 (t-90) REVERT: Z 101 LYS cc_start: 0.7526 (pttt) cc_final: 0.7087 (ptmm) REVERT: a 76 ARG cc_start: 0.5544 (mmm160) cc_final: 0.5267 (mmt90) REVERT: a 99 LEU cc_start: 0.5226 (tt) cc_final: 0.4755 (pp) REVERT: a 111 ARG cc_start: 0.3960 (ptp90) cc_final: 0.3567 (ttm110) REVERT: c 33 MET cc_start: 0.7105 (mmm) cc_final: 0.6226 (mmm) REVERT: d 16 LYS cc_start: 0.5180 (tptm) cc_final: 0.4707 (mmmm) REVERT: d 29 GLN cc_start: 0.5986 (pp30) cc_final: 0.5393 (pp30) REVERT: d 54 ASP cc_start: 0.6108 (p0) cc_final: 0.5554 (t0) REVERT: f 109 MET cc_start: 0.6307 (tmm) cc_final: 0.5673 (tmm) REVERT: g 132 MET cc_start: 0.1299 (tmm) cc_final: 0.0998 (tmm) REVERT: h 21 ILE cc_start: 0.5581 (mm) cc_final: 0.5190 (mm) REVERT: h 79 LEU cc_start: 0.5600 (tp) cc_final: 0.4989 (tp) REVERT: h 129 ILE cc_start: 0.6470 (mm) cc_final: 0.6213 (mm) REVERT: h 184 LEU cc_start: 0.6213 (tp) cc_final: 0.5084 (pt) outliers start: 1 outliers final: 0 residues processed: 715 average time/residue: 0.7282 time to fit residues: 905.8060 Evaluate side-chains 583 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 577 optimal weight: 9.9990 chunk 608 optimal weight: 0.8980 chunk 555 optimal weight: 7.9990 chunk 591 optimal weight: 9.9990 chunk 356 optimal weight: 7.9990 chunk 257 optimal weight: 0.0000 chunk 464 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 534 optimal weight: 6.9990 chunk 559 optimal weight: 0.9990 chunk 589 optimal weight: 9.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN H 59 GLN H 227 GLN I 33 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS L 84 HIS Q 114 HIS ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN ** b 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 84105 Z= 0.153 Angle : 0.580 10.018 122449 Z= 0.295 Chirality : 0.036 0.246 15194 Planarity : 0.004 0.051 8634 Dihedral : 23.570 178.633 34536 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.05 % Allowed : 1.02 % Favored : 98.93 % 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: -1.50 (0.12), residues: 4821 helix: 0.51 (0.13), residues: 1513 sheet: -1.32 (0.19), residues: 748 loop : -1.87 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP h 43 HIS 0.008 0.001 HIS Q 54 PHE 0.027 0.001 PHE E 17 TYR 0.021 0.001 TYR Q 37 ARG 0.008 0.000 ARG D 194 *********************** 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 733 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 731 time to evaluate : 4.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 ASP cc_start: 0.7003 (t0) cc_final: 0.6424 (t70) REVERT: B 139 TYR cc_start: 0.7699 (m-80) cc_final: 0.7391 (m-10) REVERT: B 148 CYS cc_start: 0.8281 (m) cc_final: 0.7267 (p) REVERT: C 122 GLU cc_start: 0.6430 (mp0) cc_final: 0.6128 (mp0) REVERT: C 217 MET cc_start: 0.6266 (ttt) cc_final: 0.5679 (ttm) REVERT: D 68 ARG cc_start: 0.7867 (tpt170) cc_final: 0.7555 (tpt90) REVERT: D 113 GLN cc_start: 0.6305 (mt0) cc_final: 0.5085 (mm-40) REVERT: E 65 ARG cc_start: 0.5300 (tpt-90) cc_final: 0.4443 (tpp80) REVERT: E 69 LEU cc_start: 0.8116 (mm) cc_final: 0.7852 (mm) REVERT: E 210 ILE cc_start: 0.7779 (mp) cc_final: 0.7457 (tt) REVERT: F 181 CYS cc_start: 0.6693 (p) cc_final: 0.6292 (p) REVERT: G 89 THR cc_start: 0.7997 (p) cc_final: 0.7406 (t) REVERT: H 1 MET cc_start: 0.7137 (tpp) cc_final: 0.6854 (mmm) REVERT: H 28 TYR cc_start: 0.5811 (m-80) cc_final: 0.5526 (m-80) REVERT: H 63 MET cc_start: 0.6635 (tpt) cc_final: 0.6366 (tpt) REVERT: H 218 LYS cc_start: 0.4549 (tmmt) cc_final: 0.4307 (ptmm) REVERT: I 46 THR cc_start: 0.8496 (p) cc_final: 0.8144 (t) REVERT: I 97 GLN cc_start: 0.6764 (mm110) cc_final: 0.6492 (mm110) REVERT: I 131 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7306 (tm-30) REVERT: J 80 ASP cc_start: 0.7581 (t0) cc_final: 0.7219 (m-30) REVERT: L 59 LYS cc_start: 0.6847 (mtpt) cc_final: 0.6537 (mtpt) REVERT: L 69 TRP cc_start: 0.6069 (m-90) cc_final: 0.5791 (m-90) REVERT: L 71 LEU cc_start: 0.7203 (mt) cc_final: 0.6251 (tt) REVERT: M 103 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7091 (tm-30) REVERT: M 118 ARG cc_start: 0.5200 (tpp-160) cc_final: 0.4786 (tpp80) REVERT: O 38 TYR cc_start: 0.7292 (m-80) cc_final: 0.7027 (m-80) REVERT: O 128 TYR cc_start: 0.8286 (t80) cc_final: 0.7993 (t80) REVERT: O 142 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7099 (mp0) REVERT: P 60 MET cc_start: 0.6679 (ptm) cc_final: 0.6396 (ptm) REVERT: P 90 ILE cc_start: 0.6603 (mm) cc_final: 0.6331 (mt) REVERT: P 116 LEU cc_start: 0.8610 (mt) cc_final: 0.8217 (pp) REVERT: P 130 GLU cc_start: 0.5296 (pm20) cc_final: 0.4963 (pm20) REVERT: Q 37 TYR cc_start: 0.5951 (p90) cc_final: 0.5142 (p90) REVERT: Q 41 GLN cc_start: 0.7803 (mp10) cc_final: 0.7411 (mp10) REVERT: Q 89 MET cc_start: 0.6913 (ptt) cc_final: 0.6277 (ttt) REVERT: Q 90 VAL cc_start: 0.5441 (t) cc_final: 0.5164 (p) REVERT: Q 94 VAL cc_start: 0.5687 (t) cc_final: 0.5111 (t) REVERT: Q 119 PHE cc_start: 0.5364 (m-10) cc_final: 0.4613 (m-80) REVERT: R 16 LYS cc_start: 0.7411 (tmmt) cc_final: 0.7188 (tmtt) REVERT: R 106 LYS cc_start: 0.7526 (pttp) cc_final: 0.7248 (pttp) REVERT: S 24 LEU cc_start: 0.7455 (mm) cc_final: 0.7146 (mm) REVERT: S 58 MET cc_start: 0.7127 (mmp) cc_final: 0.6135 (ttp) REVERT: T 58 GLU cc_start: 0.5542 (tp30) cc_final: 0.5188 (tp30) REVERT: T 83 PHE cc_start: 0.6152 (t80) cc_final: 0.5538 (t80) REVERT: T 103 LEU cc_start: 0.7433 (mm) cc_final: 0.6894 (pp) REVERT: T 134 GLN cc_start: 0.6999 (mp10) cc_final: 0.6756 (mp10) REVERT: U 128 GLN cc_start: 0.7719 (pt0) cc_final: 0.6893 (tm-30) REVERT: V 81 GLN cc_start: 0.6230 (tt0) cc_final: 0.5890 (tt0) REVERT: W 12 TYR cc_start: 0.7757 (p90) cc_final: 0.7424 (p90) REVERT: W 69 ILE cc_start: 0.7947 (tp) cc_final: 0.7684 (tt) REVERT: X 91 ASN cc_start: 0.7769 (t0) cc_final: 0.7343 (t0) REVERT: Y 23 HIS cc_start: 0.6479 (t-170) cc_final: 0.6212 (t-90) REVERT: a 76 ARG cc_start: 0.5441 (mmm160) cc_final: 0.5183 (mmt90) REVERT: a 109 TYR cc_start: 0.4366 (m-10) cc_final: 0.4093 (m-10) REVERT: a 111 ARG cc_start: 0.3749 (ptp90) cc_final: 0.3388 (ttm110) REVERT: c 33 MET cc_start: 0.7144 (mmm) cc_final: 0.6269 (mmm) REVERT: d 16 LYS cc_start: 0.5116 (tptm) cc_final: 0.4661 (mmmm) REVERT: d 54 ASP cc_start: 0.6006 (p0) cc_final: 0.5552 (t0) REVERT: e 34 TYR cc_start: 0.5253 (m-10) cc_final: 0.4839 (m-80) REVERT: f 109 MET cc_start: 0.6277 (tmm) cc_final: 0.5654 (tmm) REVERT: g 132 MET cc_start: 0.1234 (tmm) cc_final: 0.0912 (tmm) REVERT: h 21 ILE cc_start: 0.5511 (mm) cc_final: 0.5136 (mm) REVERT: h 79 LEU cc_start: 0.5811 (tp) cc_final: 0.5276 (tp) REVERT: h 129 ILE cc_start: 0.6461 (mm) cc_final: 0.6186 (mm) REVERT: h 184 LEU cc_start: 0.6157 (tp) cc_final: 0.4947 (pt) REVERT: n 13 LEU cc_start: 0.7254 (mt) cc_final: 0.7001 (mt) outliers start: 2 outliers final: 1 residues processed: 733 average time/residue: 0.7423 time to fit residues: 951.0694 Evaluate side-chains 578 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 577 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 388 optimal weight: 3.9990 chunk 625 optimal weight: 0.3980 chunk 382 optimal weight: 20.0000 chunk 296 optimal weight: 9.9990 chunk 435 optimal weight: 20.0000 chunk 656 optimal weight: 20.0000 chunk 604 optimal weight: 0.6980 chunk 522 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 403 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 141 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN H 227 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS L 50 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 GLN ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN Z 22 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 84105 Z= 0.162 Angle : 0.582 9.894 122449 Z= 0.295 Chirality : 0.036 0.249 15194 Planarity : 0.004 0.054 8634 Dihedral : 23.514 179.188 34536 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.02 % Allowed : 0.31 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.41 (0.12), residues: 4821 helix: 0.58 (0.13), residues: 1509 sheet: -1.28 (0.19), residues: 746 loop : -1.81 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP h 43 HIS 0.009 0.001 HIS L 84 PHE 0.023 0.002 PHE C 25 TYR 0.030 0.001 TYR S 84 ARG 0.008 0.000 ARG D 194 ********************** 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 713 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 712 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 ASP cc_start: 0.7092 (t0) cc_final: 0.6586 (t70) REVERT: B 139 TYR cc_start: 0.7750 (m-80) cc_final: 0.7413 (m-10) REVERT: B 183 LEU cc_start: 0.9106 (mm) cc_final: 0.8860 (mt) REVERT: C 217 MET cc_start: 0.6081 (ttt) cc_final: 0.5567 (ttm) REVERT: D 68 ARG cc_start: 0.7772 (tpt170) cc_final: 0.7505 (tpt90) REVERT: D 113 GLN cc_start: 0.6261 (mt0) cc_final: 0.5086 (mm-40) REVERT: E 65 ARG cc_start: 0.5341 (tpt-90) cc_final: 0.4481 (tpp80) REVERT: E 69 LEU cc_start: 0.8121 (mm) cc_final: 0.7861 (mm) REVERT: E 210 ILE cc_start: 0.7763 (mp) cc_final: 0.7479 (tt) REVERT: F 181 CYS cc_start: 0.6674 (p) cc_final: 0.6299 (p) REVERT: G 88 MET cc_start: 0.6664 (ttt) cc_final: 0.6435 (ttt) REVERT: G 89 THR cc_start: 0.7996 (p) cc_final: 0.7310 (t) REVERT: H 1 MET cc_start: 0.7048 (tpp) cc_final: 0.6797 (mmm) REVERT: H 28 TYR cc_start: 0.5797 (m-80) cc_final: 0.5412 (m-80) REVERT: H 63 MET cc_start: 0.6685 (tpt) cc_final: 0.6429 (tpt) REVERT: H 218 LYS cc_start: 0.4626 (tmmt) cc_final: 0.4387 (ptmm) REVERT: I 46 THR cc_start: 0.8388 (p) cc_final: 0.8102 (t) REVERT: I 97 GLN cc_start: 0.6807 (mm110) cc_final: 0.6556 (mm110) REVERT: I 131 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7288 (tm-30) REVERT: J 80 ASP cc_start: 0.7591 (t0) cc_final: 0.7213 (m-30) REVERT: K 105 PHE cc_start: 0.6487 (m-80) cc_final: 0.6231 (m-80) REVERT: L 69 TRP cc_start: 0.6001 (m-90) cc_final: 0.5777 (m-90) REVERT: L 71 LEU cc_start: 0.7197 (mt) cc_final: 0.6251 (tt) REVERT: M 103 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7146 (tm-30) REVERT: M 118 ARG cc_start: 0.5237 (tpp-160) cc_final: 0.4821 (tpp80) REVERT: O 55 ARG cc_start: 0.5919 (tmm-80) cc_final: 0.5240 (tmm-80) REVERT: O 128 TYR cc_start: 0.8274 (t80) cc_final: 0.7928 (t80) REVERT: O 142 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7131 (mp0) REVERT: P 60 MET cc_start: 0.6729 (ptm) cc_final: 0.6463 (ptm) REVERT: P 90 ILE cc_start: 0.6771 (mm) cc_final: 0.6378 (mt) REVERT: P 116 LEU cc_start: 0.8624 (mt) cc_final: 0.8233 (pp) REVERT: Q 41 GLN cc_start: 0.7899 (mp10) cc_final: 0.7417 (mp10) REVERT: Q 89 MET cc_start: 0.6953 (ptt) cc_final: 0.6311 (ttt) REVERT: Q 90 VAL cc_start: 0.5520 (t) cc_final: 0.5249 (p) REVERT: R 16 LYS cc_start: 0.7431 (tmmt) cc_final: 0.7175 (tmtt) REVERT: R 42 ILE cc_start: 0.6840 (mm) cc_final: 0.6623 (mm) REVERT: S 24 LEU cc_start: 0.7448 (mm) cc_final: 0.7027 (mm) REVERT: S 58 MET cc_start: 0.7193 (mmp) cc_final: 0.6245 (ttp) REVERT: T 58 GLU cc_start: 0.5551 (tp30) cc_final: 0.5222 (tp30) REVERT: T 83 PHE cc_start: 0.6216 (t80) cc_final: 0.5588 (t80) REVERT: T 103 LEU cc_start: 0.7436 (mm) cc_final: 0.6881 (pp) REVERT: T 134 GLN cc_start: 0.7012 (mp10) cc_final: 0.6766 (mp10) REVERT: U 128 GLN cc_start: 0.7823 (pt0) cc_final: 0.7003 (tm-30) REVERT: W 69 ILE cc_start: 0.8013 (tp) cc_final: 0.7722 (tt) REVERT: X 91 ASN cc_start: 0.7764 (t0) cc_final: 0.7360 (t0) REVERT: Y 23 HIS cc_start: 0.6496 (t-170) cc_final: 0.6280 (t-90) REVERT: Y 69 CYS cc_start: 0.7104 (p) cc_final: 0.6612 (p) REVERT: Z 74 MET cc_start: 0.5341 (mtt) cc_final: 0.4876 (ttm) REVERT: Z 114 MET cc_start: 0.7818 (mmm) cc_final: 0.7127 (mpp) REVERT: a 111 ARG cc_start: 0.3766 (ptp90) cc_final: 0.3336 (ttm110) REVERT: c 33 MET cc_start: 0.7009 (mmm) cc_final: 0.6566 (mmm) REVERT: d 16 LYS cc_start: 0.4951 (tptm) cc_final: 0.4517 (mmmm) REVERT: d 54 ASP cc_start: 0.5979 (p0) cc_final: 0.5521 (t0) REVERT: e 34 TYR cc_start: 0.5367 (m-10) cc_final: 0.4805 (m-80) REVERT: f 109 MET cc_start: 0.6337 (tmm) cc_final: 0.5672 (tmm) REVERT: g 132 MET cc_start: 0.1235 (tmm) cc_final: 0.0908 (tmm) REVERT: h 21 ILE cc_start: 0.5511 (mm) cc_final: 0.5118 (mm) REVERT: h 79 LEU cc_start: 0.5713 (tp) cc_final: 0.5232 (tp) REVERT: h 129 ILE cc_start: 0.6469 (mm) cc_final: 0.6182 (mm) REVERT: h 184 LEU cc_start: 0.6140 (tp) cc_final: 0.4960 (pt) outliers start: 1 outliers final: 0 residues processed: 713 average time/residue: 0.7347 time to fit residues: 918.6513 Evaluate side-chains 577 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 415 optimal weight: 0.6980 chunk 556 optimal weight: 1.9990 chunk 160 optimal weight: 30.0000 chunk 482 optimal weight: 0.0970 chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 30.0000 chunk 523 optimal weight: 0.6980 chunk 219 optimal weight: 20.0000 chunk 537 optimal weight: 0.0050 chunk 66 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN H 227 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 84 HIS M 5 GLN M 94 HIS Q 114 HIS ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN W 47 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.081394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066163 restraints weight = 363670.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067847 restraints weight = 193958.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.068361 restraints weight = 104863.551| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 84105 Z= 0.130 Angle : 0.544 9.971 122449 Z= 0.274 Chirality : 0.034 0.247 15194 Planarity : 0.004 0.050 8634 Dihedral : 23.354 179.610 34536 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.05 % Allowed : 0.33 % 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: -1.27 (0.12), residues: 4821 helix: 0.66 (0.13), residues: 1523 sheet: -1.06 (0.19), residues: 774 loop : -1.77 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP h 170 HIS 0.010 0.001 HIS L 84 PHE 0.027 0.001 PHE E 17 TYR 0.051 0.001 TYR h 194 ARG 0.008 0.000 ARG e 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14862.28 seconds wall clock time: 261 minutes 2.08 seconds (15662.08 seconds total)