Starting phenix.real_space_refine (version: dev) on Sun May 15 19:09:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7a_30297/05_2022/7c7a_30297.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7a_30297/05_2022/7c7a_30297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7a_30297/05_2022/7c7a_30297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7a_30297/05_2022/7c7a_30297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7a_30297/05_2022/7c7a_30297.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7a_30297/05_2022/7c7a_30297.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 27500 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 6988 Classifications: {'RNA': 330} Modifications used: {'rna3p_pyr': 147, 'rna2p_pur': 21, 'rna3p_pur': 139, 'rna2p_pyr': 23} Link IDs: {'rna3p': 285, 'rna2p': 44} Chain breaks: 1 Chain: "B" Number of atoms: 6453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6453 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 37, 'TRANS': 755} Chain breaks: 3 Chain: "C" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1246 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 11, 'TRANS': 140} Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2086 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 1 Chain: "E" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1135 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain: "F" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1271 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "I" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "J" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2253 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "K" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 840 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1110 Classifications: {'peptide': 131} Link IDs: {'TRANS': 130} Chain: "R" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'rna3p_pyr': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna2p_pyr': 1} Link IDs: {'rna3p': 6, 'rna2p': 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25888 SG CYS K 64 52.147 52.393 52.779 1.00130.63 S ATOM 26117 SG CYS K 109 49.422 50.218 54.715 1.00152.26 S Time building chain proxies: 14.68, per 1000 atoms: 0.53 Number of scatterers: 27500 At special positions: 0 Unit cell: (140.8, 133.1, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 108 16.00 P 339 15.00 Mg 3 11.99 O 6101 8.00 N 4847 7.00 C 16101 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 - 3.50 Amino acid : False - 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: 11.44 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN K 200 " pdb="ZN ZN K 200 " - pdb=" SG CYS K 109 " pdb="ZN ZN K 200 " - pdb=" SG CYS K 64 " 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 18 sheets defined 45.9% alpha, 17.4% beta 43 base pairs and 131 stacking pairs defined. Time for finding SS restraints: 8.20 Creating SS restraints... Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.619A pdb=" N ARG B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 78 Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 143 through 163 removed outlier: 3.738A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.525A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.628A pdb=" N LYS B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 227 through 235 removed outlier: 3.515A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.662A pdb=" N HIS B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.691A pdb=" N SER B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 371 through 384 removed outlier: 4.302A pdb=" N GLN B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 416 removed outlier: 3.697A pdb=" N SER B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 432 removed outlier: 3.923A pdb=" N MET B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 471 through 479 removed outlier: 4.196A pdb=" N ILE B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 564 through 574 removed outlier: 3.735A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 594 removed outlier: 3.615A pdb=" N ASN B 593 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 602 Processing helix chain 'B' and resid 605 through 627 removed outlier: 3.533A pdb=" N TYR B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 678 removed outlier: 4.128A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 718 removed outlier: 3.684A pdb=" N VAL B 706 " --> pdb=" O CYS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 788 through 798 removed outlier: 4.228A pdb=" N TRP B 792 " --> pdb=" O ASP B 788 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 850 Processing helix chain 'C' and resid 40 through 57 removed outlier: 4.492A pdb=" N HIS C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.628A pdb=" N ASN C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'D' and resid 3 through 17 removed outlier: 4.231A pdb=" N LYS D 15 " --> pdb=" O CYS D 11 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 68 through 111 removed outlier: 3.726A pdb=" N ILE D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.969A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.813A pdb=" N TYR D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU D 131 " --> pdb=" O PRO D 127 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 132 " --> pdb=" O THR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 140 through 155 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 273 through 279 removed outlier: 3.901A pdb=" N ILE D 277 " --> pdb=" O MET D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.766A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 60 removed outlier: 3.544A pdb=" N ILE E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.585A pdb=" N CYS E 68 " --> pdb=" O GLY E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 122 through 145 removed outlier: 3.677A pdb=" N ILE E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 4.112A pdb=" N CYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.939A pdb=" N LYS F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 104 removed outlier: 4.529A pdb=" N LYS F 90 " --> pdb=" O PRO F 86 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 59 removed outlier: 4.817A pdb=" N HIS G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 85 removed outlier: 3.783A pdb=" N ASP G 84 " --> pdb=" O CYS G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 27 Processing helix chain 'H' and resid 30 through 46 Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'H' and resid 73 through 82 removed outlier: 3.866A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.571A pdb=" N ASP H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 37 Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 69 through 76 Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.896A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE I 104 " --> pdb=" O ILE I 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 104' Processing helix chain 'I' and resid 113 through 123 Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.637A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.655A pdb=" N ARG I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 185 removed outlier: 4.265A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 201 removed outlier: 4.015A pdb=" N CYS I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 217 through 242 removed outlier: 3.610A pdb=" N SER I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA I 229 " --> pdb=" O MET I 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 37 removed outlier: 3.588A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 removed outlier: 4.467A pdb=" N ASP J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 104 removed outlier: 3.776A pdb=" N ILE J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 Processing helix chain 'J' and resid 142 through 153 removed outlier: 4.065A pdb=" N ILE J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.718A pdb=" N LEU J 164 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 185 removed outlier: 4.456A pdb=" N ARG J 171 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG J 185 " --> pdb=" O ILE J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.632A pdb=" N CYS J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 217 through 239 removed outlier: 3.599A pdb=" N LEU J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA J 229 " --> pdb=" O MET J 225 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER J 230 " --> pdb=" O GLY J 226 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY J 236 " --> pdb=" O VAL J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 21 removed outlier: 3.853A pdb=" N LYS K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 Processing helix chain 'K' and resid 29 through 47 removed outlier: 3.613A pdb=" N ARG K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR K 47 " --> pdb=" O SER K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 58 removed outlier: 4.526A pdb=" N GLY K 58 " --> pdb=" O GLN K 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 29 removed outlier: 3.686A pdb=" N ARG L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASN L 27 " --> pdb=" O HIS L 23 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN L 28 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 59 removed outlier: 3.634A pdb=" N GLY L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN L 44 " --> pdb=" O GLU L 40 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU L 51 " --> pdb=" O GLN L 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG L 55 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG L 56 " --> pdb=" O PHE L 52 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA L 59 " --> pdb=" O ARG L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 75 removed outlier: 4.181A pdb=" N GLN L 75 " --> pdb=" O HIS L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 95 removed outlier: 3.936A pdb=" N ILE L 93 " --> pdb=" O PHE L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 131 removed outlier: 3.822A pdb=" N THR L 104 " --> pdb=" O THR L 100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU L 115 " --> pdb=" O ASN L 111 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR L 125 " --> pdb=" O GLU L 121 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU L 126 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY L 131 " --> pdb=" O PHE L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 254 removed outlier: 6.517A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 450 Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 340 removed outlier: 5.940A pdb=" N SER B 340 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 295 " --> pdb=" O CYS B 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 762 through 769 removed outlier: 4.760A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B 835 " --> pdb=" O TYR B 829 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR B 829 " --> pdb=" O ASN B 835 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET B 837 " --> pdb=" O GLY B 827 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY B 827 " --> pdb=" O MET B 837 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 839 " --> pdb=" O THR B 825 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 823 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE B 821 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 781 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE B 823 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 779 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'D' and resid 197 through 199 removed outlier: 8.044A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 246 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 234 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 197 through 199 removed outlier: 8.044A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 246 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 234 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 202 through 203 removed outlier: 4.627A pdb=" N TRP D 202 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE D 209 " --> pdb=" O TRP D 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 73 through 78 removed outlier: 6.781A pdb=" N ILE E 85 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE E 77 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR E 83 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.094A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 138 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER F 83 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.094A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AB5, first strand: chain 'H' and resid 55 through 61 removed outlier: 9.028A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 55 through 61 removed outlier: 9.028A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER H 103 " --> pdb=" O TYR H 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.537A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR I 46 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL I 47 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU I 110 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU I 86 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL I 107 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR I 130 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA I 109 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLY I 192 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE I 158 " --> pdb=" O GLY I 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.179A pdb=" N VAL J 3 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA J 42 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU J 5 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN J 44 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL J 7 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR J 46 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE J 41 " --> pdb=" O TYR J 81 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ARG J 83 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE J 43 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR J 85 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE J 45 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE J 87 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL J 47 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ILE J 106 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER J 82 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ALA J 108 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE J 84 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL J 107 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N THR J 130 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA J 109 " --> pdb=" O THR J 130 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 92 through 95 removed outlier: 3.729A pdb=" N SER K 94 " --> pdb=" O ASN K 105 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 131 stacking parallelities Total time for adding SS restraints: 11.41 Time building geometry restraints manager: 12.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7450 1.34 - 1.46: 6731 1.46 - 1.58: 13692 1.58 - 1.70: 675 1.70 - 1.81: 162 Bond restraints: 28710 Sorted by residual: bond pdb=" C ASN B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 1.337 1.360 -0.024 9.80e-03 1.04e+04 5.75e+00 bond pdb=" CA ILE C 58 " pdb=" CB ILE C 58 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.17e+00 bond pdb=" N LEU L 62 " pdb=" CA LEU L 62 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.87e+00 bond pdb=" O5' G A 80 " pdb=" C5' G A 80 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.86e+00 bond pdb=" O5' U A 77 " pdb=" C5' U A 77 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.85e+00 ... (remaining 28705 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.92: 2415 106.92 - 113.69: 16574 113.69 - 120.46: 10797 120.46 - 127.22: 9757 127.22 - 133.99: 817 Bond angle restraints: 40360 Sorted by residual: angle pdb=" N PHE C 27 " pdb=" CA PHE C 27 " pdb=" C PHE C 27 " ideal model delta sigma weight residual 112.93 107.15 5.78 1.33e+00 5.65e-01 1.89e+01 angle pdb=" N HIS K 22 " pdb=" CA HIS K 22 " pdb=" C HIS K 22 " ideal model delta sigma weight residual 111.96 117.97 -6.01 1.41e+00 5.03e-01 1.82e+01 angle pdb=" C LYS K 100 " pdb=" N CYS K 101 " pdb=" CA CYS K 101 " ideal model delta sigma weight residual 121.64 128.58 -6.94 1.70e+00 3.46e-01 1.67e+01 angle pdb=" N ILE B 641 " pdb=" CA ILE B 641 " pdb=" C ILE B 641 " ideal model delta sigma weight residual 111.67 108.08 3.59 9.50e-01 1.11e+00 1.43e+01 angle pdb=" N ARG D 269 " pdb=" CA ARG D 269 " pdb=" C ARG D 269 " ideal model delta sigma weight residual 114.75 110.05 4.70 1.26e+00 6.30e-01 1.39e+01 ... (remaining 40355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 16394 35.38 - 70.76: 339 70.76 - 106.14: 20 106.14 - 141.51: 3 141.51 - 176.89: 14 Dihedral angle restraints: 16770 sinusoidal: 9382 harmonic: 7388 Sorted by residual: dihedral pdb=" C4' U A 143 " pdb=" C3' U A 143 " pdb=" C2' U A 143 " pdb=" C1' U A 143 " ideal model delta sinusoidal sigma weight residual -35.00 33.79 -68.79 1 8.00e+00 1.56e-02 9.57e+01 dihedral pdb=" CA HIS K 22 " pdb=" C HIS K 22 " pdb=" N VAL K 23 " pdb=" CA VAL K 23 " ideal model delta harmonic sigma weight residual -180.00 -131.15 -48.85 0 5.00e+00 4.00e-02 9.54e+01 dihedral pdb=" C5' U A 143 " pdb=" C4' U A 143 " pdb=" C3' U A 143 " pdb=" O3' U A 143 " ideal model delta sinusoidal sigma weight residual 147.00 82.73 64.27 1 8.00e+00 1.56e-02 8.49e+01 ... (remaining 16767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4413 0.060 - 0.120: 373 0.120 - 0.180: 42 0.180 - 0.240: 3 0.240 - 0.301: 1 Chirality restraints: 4832 Sorted by residual: chirality pdb=" C3' U A 143 " pdb=" C4' U A 143 " pdb=" O3' U A 143 " pdb=" C2' U A 143 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C2' U A 143 " pdb=" C3' U A 143 " pdb=" O2' U A 143 " pdb=" C1' U A 143 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C3' G A 79 " pdb=" C4' G A 79 " pdb=" O3' G A 79 " pdb=" C2' G A 79 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 4829 not shown) Planarity restraints: 3869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 614 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C PHE B 614 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE B 614 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR B 615 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 301 " -0.024 2.00e-02 2.50e+03 1.10e-02 3.32e+00 pdb=" N9 A A 301 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A A 301 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A A 301 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 301 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 301 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A A 301 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A A 301 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 301 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 301 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A A 301 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 14 " -0.023 2.00e-02 2.50e+03 1.07e-02 3.12e+00 pdb=" N9 A A 14 " 0.025 2.00e-02 2.50e+03 pdb=" C8 A A 14 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 14 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 14 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A 14 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A A 14 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A A 14 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A A 14 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 14 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A A 14 " 0.002 2.00e-02 2.50e+03 ... (remaining 3866 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1153 2.71 - 3.25: 25404 3.25 - 3.80: 44095 3.80 - 4.35: 57500 4.35 - 4.90: 88238 Nonbonded interactions: 216390 Sorted by model distance: nonbonded pdb=" O2' A A 25 " pdb=" OP2 A A 26 " model vdw 2.157 2.440 nonbonded pdb=" OP1 G A 87 " pdb="MG MG R 101 " model vdw 2.171 2.170 nonbonded pdb=" OP2 A A 86 " pdb="MG MG A 401 " model vdw 2.172 2.170 nonbonded pdb=" OP1 A A 86 " pdb="MG MG A 402 " model vdw 2.178 2.170 nonbonded pdb=" O2' A A 37 " pdb=" O VAL G 35 " model vdw 2.182 2.440 ... (remaining 216385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 339 5.49 5 Mg 3 5.21 5 S 108 5.16 5 C 16101 2.51 5 N 4847 2.21 5 O 6101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.020 Extract box with map and model: 19.270 Check model and map are aligned: 0.380 Convert atoms to be neutral: 0.220 Process input model: 81.520 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 28710 Z= 0.142 Angle : 0.582 8.861 40360 Z= 0.358 Chirality : 0.035 0.301 4832 Planarity : 0.003 0.041 3869 Dihedral : 14.301 176.894 11970 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.00 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.84 (0.15), residues: 2485 helix: -1.09 (0.14), residues: 1039 sheet: -0.64 (0.26), residues: 374 loop : -3.18 (0.16), residues: 1072 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 613 time to evaluate : 2.536 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 outliers start: 1 outliers final: 0 residues processed: 613 average time/residue: 1.3526 time to fit residues: 960.7243 Evaluate side-chains 276 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.904 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 178 ASN B 180 HIS B 201 ASN B 323 ASN B 371 HIS B 377 GLN B 570 HIS B 595 GLN B 803 ASN C 32 HIS C 59 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 99 ASN D 190 ASN F 52 ASN F 89 GLN G 56 HIS G 85 GLN H 27 HIS ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN I 172 GLN I 235 ASN K 28 ASN K 41 HIS L 22 ASN L 25 ASN L 58 GLN L 90 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 28710 Z= 0.273 Angle : 0.691 9.360 40360 Z= 0.357 Chirality : 0.041 0.297 4832 Planarity : 0.007 0.114 3869 Dihedral : 13.614 179.341 6802 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.84 % Rotamer Outliers : 4.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.60 (0.16), residues: 2485 helix: 0.24 (0.16), residues: 1046 sheet: -0.16 (0.26), residues: 387 loop : -2.85 (0.16), residues: 1052 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 327 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 33 residues processed: 395 average time/residue: 1.2719 time to fit residues: 591.8032 Evaluate side-chains 286 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 2.788 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 26 residues processed: 9 average time/residue: 0.6073 time to fit residues: 11.0669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 256 optimal weight: 0.0050 chunk 277 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 205 optimal weight: 5.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 135 GLN D 197 GLN F 45 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 HIS H 27 HIS ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 28710 Z= 0.186 Angle : 0.576 10.202 40360 Z= 0.294 Chirality : 0.037 0.211 4832 Planarity : 0.005 0.117 3869 Dihedral : 13.352 178.709 6802 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer Outliers : 4.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.00 (0.17), residues: 2485 helix: 0.83 (0.16), residues: 1050 sheet: 0.28 (0.26), residues: 387 loop : -2.72 (0.17), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 275 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 40 residues processed: 341 average time/residue: 1.2461 time to fit residues: 503.1292 Evaluate side-chains 280 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 240 time to evaluate : 2.749 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 35 residues processed: 6 average time/residue: 0.5254 time to fit residues: 7.9770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 850 GLN C 59 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN E 59 ASN E 139 ASN F 45 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 28710 Z= 0.230 Angle : 0.616 9.353 40360 Z= 0.318 Chirality : 0.039 0.262 4832 Planarity : 0.006 0.106 3869 Dihedral : 13.476 179.507 6802 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.04 % Favored : 92.88 % Rotamer Outliers : 5.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2485 helix: 1.00 (0.16), residues: 1045 sheet: 0.46 (0.26), residues: 386 loop : -2.60 (0.17), residues: 1054 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 286 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 52 residues processed: 378 average time/residue: 1.2519 time to fit residues: 561.3554 Evaluate side-chains 293 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 241 time to evaluate : 2.724 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 42 residues processed: 13 average time/residue: 0.6094 time to fit residues: 14.3627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 232 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 GLN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 27 HIS ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.100 28710 Z= 0.202 Angle : 0.591 10.374 40360 Z= 0.302 Chirality : 0.037 0.227 4832 Planarity : 0.005 0.095 3869 Dihedral : 13.365 179.564 6802 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.88 % Favored : 94.08 % Rotamer Outliers : 5.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2485 helix: 1.20 (0.17), residues: 1040 sheet: 0.62 (0.26), residues: 381 loop : -2.56 (0.17), residues: 1064 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 253 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 64 residues processed: 350 average time/residue: 1.2335 time to fit residues: 513.1484 Evaluate side-chains 298 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 234 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 54 residues processed: 12 average time/residue: 0.6807 time to fit residues: 14.8073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 chunk 226 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 27 HIS H 128 GLN ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 GLN ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.114 28710 Z= 0.224 Angle : 0.609 11.688 40360 Z= 0.311 Chirality : 0.038 0.235 4832 Planarity : 0.005 0.094 3869 Dihedral : 13.313 179.526 6802 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.68 % Favored : 93.28 % Rotamer Outliers : 4.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2485 helix: 1.25 (0.17), residues: 1044 sheet: 0.68 (0.26), residues: 381 loop : -2.51 (0.17), residues: 1060 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 244 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 60 residues processed: 325 average time/residue: 1.1711 time to fit residues: 455.9385 Evaluate side-chains 281 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 221 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 54 residues processed: 9 average time/residue: 0.7975 time to fit residues: 12.6769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 199 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 229 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN B 727 ASN ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 135 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.031 28710 Z= 0.527 Angle : 0.789 94.745 40360 Z= 0.361 Chirality : 0.038 0.448 4832 Planarity : 0.005 0.098 3869 Dihedral : 13.256 179.357 6802 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.68 % Rotamer Outliers : 4.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2485 helix: 1.32 (0.17), residues: 1041 sheet: 0.79 (0.27), residues: 377 loop : -2.47 (0.17), residues: 1067 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 240 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 62 residues processed: 317 average time/residue: 1.1518 time to fit residues: 438.4898 Evaluate side-chains 288 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 226 time to evaluate : 2.901 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 57 residues processed: 7 average time/residue: 0.8047 time to fit residues: 10.9360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 19 ASN L 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.153 28710 Z= 0.227 Angle : 0.639 15.387 40360 Z= 0.328 Chirality : 0.038 0.233 4832 Planarity : 0.005 0.093 3869 Dihedral : 13.233 179.496 6802 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.72 % Favored : 93.24 % Rotamer Outliers : 4.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2485 helix: 1.35 (0.17), residues: 1040 sheet: 0.79 (0.27), residues: 377 loop : -2.41 (0.17), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 244 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 65 residues processed: 316 average time/residue: 1.3064 time to fit residues: 490.5245 Evaluate side-chains 292 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 227 time to evaluate : 2.583 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 59 residues processed: 9 average time/residue: 0.5097 time to fit residues: 10.3623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 228 optimal weight: 0.6980 chunk 239 optimal weight: 0.4980 chunk 252 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.987 28710 Z= 0.516 Angle : 0.854 106.074 40360 Z= 0.389 Chirality : 0.039 0.400 4832 Planarity : 0.005 0.119 3869 Dihedral : 13.247 179.607 6802 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2485 helix: 1.25 (0.17), residues: 1049 sheet: 0.72 (0.27), residues: 379 loop : -2.41 (0.17), residues: 1057 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 234 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 62 residues processed: 297 average time/residue: 1.3049 time to fit residues: 461.1700 Evaluate side-chains 294 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 232 time to evaluate : 2.668 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 56 residues processed: 7 average time/residue: 0.7824 time to fit residues: 10.6179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 0.5980 chunk 267 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 258 optimal weight: 0.7980 chunk 223 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 727 ASN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.987 28710 Z= 0.569 Angle : 0.858 106.074 40360 Z= 0.393 Chirality : 0.039 0.399 4832 Planarity : 0.005 0.139 3869 Dihedral : 13.247 179.607 6802 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2485 helix: 1.25 (0.17), residues: 1049 sheet: 0.72 (0.27), residues: 379 loop : -2.41 (0.17), residues: 1057 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 231 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 56 residues processed: 286 average time/residue: 1.2645 time to fit residues: 431.9149 Evaluate side-chains 285 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 229 time to evaluate : 3.439 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 56 residues processed: 1 average time/residue: 0.4346 time to fit residues: 4.3951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 727 ASN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.122616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.089619 restraints weight = 56839.922| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.50 r_work: 0.3500 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work: 0.3479 rms_B_bonded: 2.36 restraints_weight: 0.1250 r_work: 0.3468 rms_B_bonded: 2.43 restraints_weight: 0.0625 r_work: 0.3457 rms_B_bonded: 2.53 restraints_weight: 0.0312 r_work: 0.3446 rms_B_bonded: 2.66 restraints_weight: 0.0156 r_work: 0.3434 rms_B_bonded: 2.81 restraints_weight: 0.0078 r_work: 0.3422 rms_B_bonded: 2.99 restraints_weight: 0.0039 r_work: 0.3409 rms_B_bonded: 3.19 restraints_weight: 0.0020 r_work: 0.3396 rms_B_bonded: 3.41 restraints_weight: 0.0010 r_work: 0.3382 rms_B_bonded: 3.67 restraints_weight: 0.0005 r_work: 0.3367 rms_B_bonded: 3.95 restraints_weight: 0.0002 r_work: 0.3352 rms_B_bonded: 4.26 restraints_weight: 0.0001 r_work: 0.3336 rms_B_bonded: 4.61 restraints_weight: 0.0001 r_work: 0.3319 rms_B_bonded: 5.00 restraints_weight: 0.0000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4076 r_free = 0.4076 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4076 r_free = 0.4076 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.987 28710 Z= 0.569 Angle : 0.858 106.074 40360 Z= 0.393 Chirality : 0.039 0.399 4832 Planarity : 0.005 0.139 3869 Dihedral : 13.247 179.607 6802 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2485 helix: 1.25 (0.17), residues: 1049 sheet: 0.72 (0.27), residues: 379 loop : -2.41 (0.17), residues: 1057 =============================================================================== Job complete usr+sys time: 9187.30 seconds wall clock time: 164 minutes 25.91 seconds (9865.91 seconds total)