Starting phenix.real_space_refine on Wed Mar 20 03:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvw_29494/03_2024/8fvw_29494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvw_29494/03_2024/8fvw_29494.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvw_29494/03_2024/8fvw_29494_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvw_29494/03_2024/8fvw_29494_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvw_29494/03_2024/8fvw_29494_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvw_29494/03_2024/8fvw_29494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvw_29494/03_2024/8fvw_29494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvw_29494/03_2024/8fvw_29494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fvw_29494/03_2024/8fvw_29494_updated.pdb" } resolution = 2.1 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= 0.002 sd= 0.089 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 52 5.49 5 Mg 2 5.21 5 S 107 5.16 5 Na 1 4.78 5 C 16059 2.51 5 N 4586 2.21 5 O 5299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26108 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1716 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 223, 1716 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1727 Chain: "E" Number of atoms: 1699 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1691 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 220, 1691 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1701 Chain: "F" Number of atoms: 10442 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1319, 10405 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1319, 10405 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 10528 Chain: "G" Number of atoms: 10352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 10352 Classifications: {'peptide': 1330} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1274} Chain breaks: 3 Chain: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "A" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 343 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' MG': 1, ' ZN': 2, 'G4P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14314 SG CYS G 70 113.066 97.345 92.202 1.00115.52 S ATOM 14328 SG CYS G 72 113.146 100.385 94.207 1.00113.85 S ATOM 14436 SG CYS G 85 115.656 97.523 94.990 1.00113.53 S ATOM 14460 SG CYS G 88 111.941 97.104 95.773 1.00119.07 S ATOM 20148 SG CYS G 814 88.128 35.880 87.705 1.00 48.51 S ATOM 20713 SG CYS G 888 86.635 39.124 87.668 1.00 40.76 S ATOM 20764 SG CYS G 895 87.286 37.693 84.335 1.00 39.61 S ATOM 20785 SG CYS G 898 84.602 36.615 85.881 1.00 49.52 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="NA NA H 102 " occ=0.58 residue: pdb=" O HOH G1630 " occ=0.55 residue: pdb=" O HOH G1677 " occ=0.64 residue: pdb=" O HOH H 205 " occ=0.61 Time building chain proxies: 20.17, per 1000 atoms: 0.77 Number of scatterers: 26108 At special positions: 0 Unit cell: (130.35, 159.225, 165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 107 16.00 P 52 15.00 Mg 2 11.99 Na 1 11.00 O 5299 8.00 N 4586 7.00 C 16059 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: 12.00 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G1502 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 72 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 88 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 85 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 70 " pdb=" ZN G1503 " pdb="ZN ZN G1503 " - pdb=" SG CYS G 898 " pdb="ZN ZN G1503 " - pdb=" SG CYS G 814 " pdb="ZN ZN G1503 " - pdb=" SG CYS G 895 " pdb="ZN ZN G1503 " - pdb=" SG CYS G 888 " Number of angles added : 12 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5854 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 38 sheets defined 33.2% alpha, 14.5% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 14.65 Creating SS restraints... Processing helix chain 'D' and resid 35 through 50 Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 213 through 232 removed outlier: 4.362A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 78 through 86 Processing helix chain 'E' and resid 112 through 114 No H-bonds generated for 'chain 'E' and resid 112 through 114' Processing helix chain 'E' and resid 155 through 157 No H-bonds generated for 'chain 'E' and resid 155 through 157' Processing helix chain 'E' and resid 213 through 228 removed outlier: 3.500A pdb=" N LEU E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 48 through 55 Processing helix chain 'F' and resid 82 through 88 Processing helix chain 'F' and resid 206 through 212 Processing helix chain 'F' and resid 217 through 224 Processing helix chain 'F' and resid 243 through 246 Processing helix chain 'F' and resid 271 through 278 removed outlier: 3.767A pdb=" N LEU F 277 " --> pdb=" O HIS F 273 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 294 removed outlier: 3.799A pdb=" N GLY F 294 " --> pdb=" O TYR F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 327 Processing helix chain 'F' and resid 346 through 353 Processing helix chain 'F' and resid 359 through 370 Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.707A pdb=" N GLU F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE F 389 " --> pdb=" O PHE F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 408 Processing helix chain 'F' and resid 422 through 436 Processing helix chain 'F' and resid 456 through 481 removed outlier: 3.672A pdb=" N ALA F 474 " --> pdb=" O ARG F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 492 No H-bonds generated for 'chain 'F' and resid 489 through 492' Processing helix chain 'F' and resid 496 through 508 Processing helix chain 'F' and resid 520 through 528 Processing helix chain 'F' and resid 545 through 548 No H-bonds generated for 'chain 'F' and resid 545 through 548' Processing helix chain 'F' and resid 552 through 554 No H-bonds generated for 'chain 'F' and resid 552 through 554' Processing helix chain 'F' and resid 608 through 613 removed outlier: 3.653A pdb=" N GLY F 612 " --> pdb=" O ALA F 608 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN F 613 " --> pdb=" O ILE F 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 608 through 613' Processing helix chain 'F' and resid 663 through 666 No H-bonds generated for 'chain 'F' and resid 663 through 666' Processing helix chain 'F' and resid 671 through 673 No H-bonds generated for 'chain 'F' and resid 671 through 673' Processing helix chain 'F' and resid 676 through 688 removed outlier: 4.009A pdb=" N ARG F 687 " --> pdb=" O ALA F 683 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN F 688 " --> pdb=" O ASN F 684 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 712 Processing helix chain 'F' and resid 738 through 740 No H-bonds generated for 'chain 'F' and resid 738 through 740' Processing helix chain 'F' and resid 812 through 814 No H-bonds generated for 'chain 'F' and resid 812 through 814' Processing helix chain 'F' and resid 820 through 824 Processing helix chain 'F' and resid 860 through 862 No H-bonds generated for 'chain 'F' and resid 860 through 862' Processing helix chain 'F' and resid 943 through 959 Processing helix chain 'F' and resid 962 through 979 removed outlier: 3.793A pdb=" N LEU F 967 " --> pdb=" O GLU F 963 " (cutoff:3.500A) Processing helix chain 'F' and resid 986 through 990 removed outlier: 4.110A pdb=" N ASP F 990 " --> pdb=" O ALA F 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 986 through 990' Processing helix chain 'F' and resid 1006 through 1009 No H-bonds generated for 'chain 'F' and resid 1006 through 1009' Processing helix chain 'F' and resid 1011 through 1021 removed outlier: 3.805A pdb=" N GLU F1016 " --> pdb=" O GLU F1012 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN F1017 " --> pdb=" O GLN F1013 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR F1018 " --> pdb=" O LEU F1014 " (cutoff:3.500A) Processing helix chain 'F' and resid 1029 through 1037 Processing helix chain 'F' and resid 1082 through 1084 No H-bonds generated for 'chain 'F' and resid 1082 through 1084' Processing helix chain 'F' and resid 1100 through 1104 Proline residue: F1104 - end of helix Processing helix chain 'F' and resid 1109 through 1133 removed outlier: 3.938A pdb=" N GLU F1114 " --> pdb=" O GLN F1111 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN F1129 " --> pdb=" O ASP F1126 " (cutoff:3.500A) Processing helix chain 'F' and resid 1138 through 1150 Processing helix chain 'F' and resid 1161 through 1163 No H-bonds generated for 'chain 'F' and resid 1161 through 1163' Processing helix chain 'F' and resid 1166 through 1176 Processing helix chain 'F' and resid 1192 through 1201 Processing helix chain 'F' and resid 1239 through 1242 No H-bonds generated for 'chain 'F' and resid 1239 through 1242' Processing helix chain 'F' and resid 1272 through 1281 Processing helix chain 'F' and resid 1284 through 1291 Processing helix chain 'F' and resid 1298 through 1310 Processing helix chain 'F' and resid 1321 through 1332 Processing helix chain 'G' and resid 27 through 33 Processing helix chain 'G' and resid 59 through 62 No H-bonds generated for 'chain 'G' and resid 59 through 62' Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 123 through 128 Processing helix chain 'G' and resid 132 through 139 Processing helix chain 'G' and resid 162 through 171 removed outlier: 4.187A pdb=" N LEU G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP G 167 " --> pdb=" O GLU G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 190 Processing helix chain 'G' and resid 194 through 206 removed outlier: 3.714A pdb=" N ASN G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 229 Processing helix chain 'G' and resid 234 through 237 Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 266 through 283 Processing helix chain 'G' and resid 289 through 307 Processing helix chain 'G' and resid 337 through 341 Processing helix chain 'G' and resid 370 through 376 Processing helix chain 'G' and resid 378 through 387 Processing helix chain 'G' and resid 394 through 403 Processing helix chain 'G' and resid 406 through 415 Processing helix chain 'G' and resid 431 through 433 No H-bonds generated for 'chain 'G' and resid 431 through 433' Processing helix chain 'G' and resid 451 through 457 removed outlier: 4.377A pdb=" N ALA G 455 " --> pdb=" O LEU G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 483 Processing helix chain 'G' and resid 486 through 488 No H-bonds generated for 'chain 'G' and resid 486 through 488' Processing helix chain 'G' and resid 505 through 514 Processing helix chain 'G' and resid 530 through 538 Processing helix chain 'G' and resid 574 through 582 removed outlier: 3.786A pdb=" N MET G 581 " --> pdb=" O ALA G 577 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE G 582 " --> pdb=" O ILE G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 589 through 591 No H-bonds generated for 'chain 'G' and resid 589 through 591' Processing helix chain 'G' and resid 598 through 612 Processing helix chain 'G' and resid 614 through 635 Processing helix chain 'G' and resid 641 through 643 No H-bonds generated for 'chain 'G' and resid 641 through 643' Processing helix chain 'G' and resid 650 through 669 Processing helix chain 'G' and resid 675 through 701 Processing helix chain 'G' and resid 721 through 728 Processing helix chain 'G' and resid 734 through 741 Processing helix chain 'G' and resid 769 through 804 removed outlier: 3.685A pdb=" N HIS G 777 " --> pdb=" O PHE G 773 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY G 778 " --> pdb=" O ILE G 774 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA G 791 " --> pdb=" O ALA G 787 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN G 792 " --> pdb=" O LEU G 788 " (cutoff:3.500A) Processing helix chain 'G' and resid 835 through 839 Processing helix chain 'G' and resid 866 through 874 Processing helix chain 'G' and resid 896 through 899 No H-bonds generated for 'chain 'G' and resid 896 through 899' Processing helix chain 'G' and resid 915 through 927 Proline residue: G 926 - end of helix Processing helix chain 'G' and resid 1069 through 1073 removed outlier: 4.079A pdb=" N ASP G1073 " --> pdb=" O ALA G1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1069 through 1073' Processing helix chain 'G' and resid 1138 through 1145 Processing helix chain 'G' and resid 1217 through 1224 Processing helix chain 'G' and resid 1226 through 1243 removed outlier: 3.501A pdb=" N VAL G1240 " --> pdb=" O GLU G1236 " (cutoff:3.500A) Processing helix chain 'G' and resid 1250 through 1261 Processing helix chain 'G' and resid 1282 through 1295 Processing helix chain 'G' and resid 1309 through 1314 Processing helix chain 'G' and resid 1319 through 1325 Processing helix chain 'G' and resid 1328 through 1338 Processing helix chain 'G' and resid 1347 through 1352 Processing helix chain 'G' and resid 1360 through 1371 removed outlier: 4.308A pdb=" N ALA G1364 " --> pdb=" O THR G1361 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG G1371 " --> pdb=" O ASP G1368 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 13 Processing helix chain 'H' and resid 16 through 31 Processing helix chain 'H' and resid 46 through 55 Processing helix chain 'H' and resid 61 through 73 Processing sheet with id= A, first strand: chain 'D' and resid 12 through 18 removed outlier: 6.663A pdb=" N THR D 27 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE D 16 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS D 25 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLN D 18 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS D 23 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.703A pdb=" N LYS D 145 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 59 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG D 143 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE D 61 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N SER D 141 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'D' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'E' and resid 13 through 20 removed outlier: 6.373A pdb=" N HIS E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 170 through 172 removed outlier: 6.657A pdb=" N LYS E 145 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL E 59 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG E 143 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE E 61 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER E 141 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 90 through 92 Processing sheet with id= H, first strand: chain 'E' and resid 108 through 111 Processing sheet with id= I, first strand: chain 'F' and resid 93 through 95 Processing sheet with id= J, first strand: chain 'F' and resid 136 through 138 Processing sheet with id= K, first strand: chain 'F' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'F' and resid 154 through 160 removed outlier: 3.671A pdb=" N LEU F 171 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR F 172 " --> pdb=" O PHE F 188 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 227 through 231 Processing sheet with id= N, first strand: chain 'F' and resid 295 through 297 removed outlier: 4.663A pdb=" N LYS F 295 " --> pdb=" O LEU F 317 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 529 through 531 Processing sheet with id= P, first strand: chain 'F' and resid 603 through 607 Processing sheet with id= Q, first strand: chain 'F' and resid 634 through 637 Processing sheet with id= R, first strand: chain 'F' and resid 748 through 752 removed outlier: 5.968A pdb=" N LYS F 735 " --> pdb=" O VAL F 724 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL F 724 " --> pdb=" O LYS F 735 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 1226 through 1232 removed outlier: 4.333A pdb=" N THR F1226 " --> pdb=" O PHE F 804 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE F1096 " --> pdb=" O ALA F 803 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 1065 through 1067 Processing sheet with id= U, first strand: chain 'F' and resid 66 through 75 removed outlier: 6.734A pdb=" N LYS F 99 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR F 73 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG F 97 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 255 through 257 removed outlier: 3.923A pdb=" N VAL F 263 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA F 257 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 816 through 819 removed outlier: 7.566A pdb=" N VAL F 818 " --> pdb=" O SER F1077 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE F1079 " --> pdb=" O VAL F 818 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 830 through 841 removed outlier: 3.670A pdb=" N ASP F 930 " --> pdb=" O TYR F1053 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA F1055 " --> pdb=" O VAL F 928 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL F 928 " --> pdb=" O ALA F1055 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 19 through 21 Processing sheet with id= Z, first strand: chain 'G' and resid 241 through 244 removed outlier: 7.438A pdb=" N HIS G 104 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU G 37 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU G 106 " --> pdb=" O GLU G 37 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 159 through 161 removed outlier: 3.827A pdb=" N ASP G 177 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 350 through 354 Processing sheet with id= AC, first strand: chain 'G' and resid 355 through 358 removed outlier: 6.070A pdb=" N ILE G 447 " --> pdb=" O THR G 356 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY G 358 " --> pdb=" O ILE G 447 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU G 449 " --> pdb=" O GLY G 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 547 through 557 Processing sheet with id= AE, first strand: chain 'G' and resid 703 through 707 Processing sheet with id= AF, first strand: chain 'G' and resid 820 through 823 Processing sheet with id= AG, first strand: chain 'G' and resid 957 through 961 removed outlier: 3.625A pdb=" N SER G 961 " --> pdb=" O GLU G 981 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU G 981 " --> pdb=" O SER G 961 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU G 993 " --> pdb=" O LEU G 984 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 1034 through 1037 Processing sheet with id= AI, first strand: chain 'G' and resid 1046 through 1049 removed outlier: 4.153A pdb=" N ALA G1105 " --> pdb=" O VAL G1061 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 1162 through 1164 Processing sheet with id= AK, first strand: chain 'G' and resid 1279 through 1281 removed outlier: 4.302A pdb=" N LYS G1263 " --> pdb=" O ASP G1305 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR G1301 " --> pdb=" O VAL G1267 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 949 through 952 removed outlier: 3.586A pdb=" N ALA G1018 " --> pdb=" O ILE G 950 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL G 952 " --> pdb=" O THR G1016 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N THR G1016 " --> pdb=" O VAL G 952 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 12.66 Time building geometry restraints manager: 12.71 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: 7141 1.33 - 1.45: 4070 1.45 - 1.57: 14876 1.57 - 1.69: 102 1.69 - 1.81: 186 Bond restraints: 26375 Sorted by residual: bond pdb=" C2' G4P G1501 " pdb=" C1' G4P G1501 " ideal model delta sigma weight residual 1.305 1.508 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" O4' G4P G1501 " pdb=" C1' G4P G1501 " ideal model delta sigma weight residual 1.613 1.424 0.189 2.00e-02 2.50e+03 8.91e+01 bond pdb=" N3 G4P G1501 " pdb=" C4 G4P G1501 " ideal model delta sigma weight residual 1.494 1.340 0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C2 G4P G1501 " pdb=" N3 G4P G1501 " ideal model delta sigma weight residual 1.489 1.337 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C4' G4P G1501 " pdb=" O4' G4P G1501 " ideal model delta sigma weight residual 1.295 1.425 -0.130 2.00e-02 2.50e+03 4.23e+01 ... (remaining 26370 not shown) Histogram of bond angle deviations from ideal: 98.63 - 106.01: 827 106.01 - 113.39: 14651 113.39 - 120.77: 11523 120.77 - 128.15: 8669 128.15 - 135.53: 185 Bond angle restraints: 35855 Sorted by residual: angle pdb=" N VAL F 56 " pdb=" CA VAL F 56 " pdb=" C VAL F 56 " ideal model delta sigma weight residual 113.53 108.39 5.14 9.80e-01 1.04e+00 2.75e+01 angle pdb=" O1C G4P G1501 " pdb=" PC G4P G1501 " pdb=" O2C G4P G1501 " ideal model delta sigma weight residual 109.42 120.64 -11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA HIS G 430 " pdb=" C HIS G 430 " pdb=" O HIS G 430 " ideal model delta sigma weight residual 121.51 117.48 4.03 1.12e+00 7.97e-01 1.30e+01 angle pdb=" PA G4P G1501 " pdb=" O3A G4P G1501 " pdb=" PB G4P G1501 " ideal model delta sigma weight residual 123.58 134.00 -10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CA ASP F1297 " pdb=" C ASP F1297 " pdb=" O ASP F1297 " ideal model delta sigma weight residual 121.66 117.73 3.93 1.17e+00 7.31e-01 1.13e+01 ... (remaining 35850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14576 17.95 - 35.91: 1177 35.91 - 53.86: 262 53.86 - 71.81: 92 71.81 - 89.77: 29 Dihedral angle restraints: 16136 sinusoidal: 7029 harmonic: 9107 Sorted by residual: dihedral pdb=" CA PHE F 57 " pdb=" C PHE F 57 " pdb=" N PRO F 58 " pdb=" CA PRO F 58 " ideal model delta harmonic sigma weight residual 0.00 24.54 -24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASP F 396 " pdb=" C ASP F 396 " pdb=" N LEU F 397 " pdb=" CA LEU F 397 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA PRO F 375 " pdb=" C PRO F 375 " pdb=" N PRO F 376 " pdb=" CA PRO F 376 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 16133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3403 0.057 - 0.115: 618 0.115 - 0.172: 68 0.172 - 0.230: 4 0.230 - 0.287: 1 Chirality restraints: 4094 Sorted by residual: chirality pdb=" CB ILE F 104 " pdb=" CA ILE F 104 " pdb=" CG1 ILE F 104 " pdb=" CG2 ILE F 104 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C2' G4P G1501 " pdb=" C3' G4P G1501 " pdb=" O2' G4P G1501 " pdb=" C1' G4P G1501 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE F 59 " pdb=" N ILE F 59 " pdb=" C ILE F 59 " pdb=" CB ILE F 59 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.66e-01 ... (remaining 4091 not shown) Planarity restraints: 4514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 322 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO G 323 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO G 323 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 323 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 242 " -0.044 5.00e-02 4.00e+02 6.76e-02 7.30e+00 pdb=" N PRO F 243 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO F 243 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 243 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 501 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO G 502 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 502 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 502 " 0.036 5.00e-02 4.00e+02 ... (remaining 4511 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 250 2.56 - 3.14: 20911 3.14 - 3.73: 43943 3.73 - 4.31: 61714 4.31 - 4.90: 98532 Nonbonded interactions: 225350 Sorted by model distance: nonbonded pdb=" O3' A C 16 " pdb="MG MG G1504 " model vdw 1.974 2.170 nonbonded pdb="MG MG H 101 " pdb=" O HOH G1630 " model vdw 2.003 2.170 nonbonded pdb="MG MG G1504 " pdb=" O HOH G1602 " model vdw 2.072 2.170 nonbonded pdb=" OD1 ASP G 460 " pdb="MG MG G1504 " model vdw 2.193 2.170 nonbonded pdb=" OG SER G 977 " pdb=" OG1 THR G 980 " model vdw 2.197 2.440 ... (remaining 225345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 7 through 43 or resid 45 through 135 or (resid 136 and (na \ me N or name CA or name C or name O or name CB )) or resid 137 through 158 or re \ sid 169 through 218 or resid 220 through 233)) selection = (chain 'E' and (resid 7 through 43 or resid 45 through 190 or (resid 191 through \ 192 and (name N or name CA or name C or name O or name CB )) or resid 193 or (r \ esid 194 and (name N or name CA or name C or name O or name CB )) or resid 195 t \ hrough 218 or resid 220 through 233)) } 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=0.30 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: 2.930 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: 0.010 Extract box with map and model: 14.540 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 96.280 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.004 0.203 26375 Z= 0.235 Angle : 0.609 11.222 35855 Z= 0.334 Chirality : 0.044 0.287 4094 Planarity : 0.005 0.073 4514 Dihedral : 14.748 89.767 10282 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.07 % Allowed : 0.30 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3150 helix: 1.02 (0.16), residues: 1115 sheet: -0.02 (0.25), residues: 400 loop : -0.06 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 807 HIS 0.006 0.001 HIS F1070 PHE 0.019 0.001 PHE F 812 TYR 0.019 0.001 TYR G 140 ARG 0.007 0.001 ARG G1148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 375 time to evaluate : 2.549 Fit side-chains REVERT: F 342 ASP cc_start: 0.6764 (p0) cc_final: 0.6544 (p0) REVERT: F 477 GLU cc_start: 0.7254 (pp20) cc_final: 0.6987 (pt0) REVERT: F 955 GLN cc_start: 0.7125 (tp40) cc_final: 0.6872 (tp-100) REVERT: F 1029 LEU cc_start: 0.7421 (tp) cc_final: 0.7057 (tp) REVERT: G 50 LYS cc_start: 0.6910 (ttpp) cc_final: 0.6697 (tttp) REVERT: G 52 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5773 (mm-30) REVERT: G 66 LYS cc_start: 0.7427 (mmtt) cc_final: 0.7182 (mtmm) REVERT: G 204 GLU cc_start: 0.6509 (tt0) cc_final: 0.6278 (tt0) REVERT: G 222 LYS cc_start: 0.7841 (tppt) cc_final: 0.7505 (tppt) REVERT: G 666 GLU cc_start: 0.7090 (tp30) cc_final: 0.6883 (tt0) REVERT: G 983 LYS cc_start: 0.6859 (mppt) cc_final: 0.6647 (mppt) REVERT: G 993 GLU cc_start: 0.6264 (mp0) cc_final: 0.5980 (mm-30) REVERT: G 1193 TRP cc_start: 0.5385 (p-90) cc_final: 0.4902 (p-90) outliers start: 2 outliers final: 0 residues processed: 377 average time/residue: 1.8693 time to fit residues: 788.7950 Evaluate side-chains 284 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 163 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 193 ASN F 834 GLN G1268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26375 Z= 0.234 Angle : 0.577 8.157 35855 Z= 0.307 Chirality : 0.044 0.169 4094 Planarity : 0.005 0.055 4514 Dihedral : 11.712 73.887 4074 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.19 % Allowed : 6.86 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3150 helix: 0.93 (0.16), residues: 1119 sheet: 0.16 (0.25), residues: 392 loop : -0.05 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 807 HIS 0.009 0.001 HIS F1070 PHE 0.018 0.002 PHE F1323 TYR 0.021 0.002 TYR F1231 ARG 0.012 0.001 ARG F1033 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 291 time to evaluate : 2.665 Fit side-chains revert: symmetry clash REVERT: F 101 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6297 (ptm160) REVERT: F 477 GLU cc_start: 0.7202 (pp20) cc_final: 0.6963 (pt0) REVERT: F 1029 LEU cc_start: 0.7457 (tp) cc_final: 0.7173 (tp) REVERT: F 1135 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: G 192 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7133 (ptm) REVERT: G 204 GLU cc_start: 0.6560 (tt0) cc_final: 0.6312 (tt0) REVERT: G 399 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7746 (mtpp) REVERT: G 660 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: G 983 LYS cc_start: 0.6844 (mppt) cc_final: 0.6572 (mppt) REVERT: G 993 GLU cc_start: 0.6487 (mp0) cc_final: 0.6043 (mm-30) REVERT: G 1193 TRP cc_start: 0.5469 (p-90) cc_final: 0.4915 (p-90) REVERT: G 1212 ASP cc_start: 0.6477 (m-30) cc_final: 0.6011 (t70) REVERT: G 1224 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.6807 (mtm-85) outliers start: 32 outliers final: 6 residues processed: 305 average time/residue: 1.8448 time to fit residues: 633.4152 Evaluate side-chains 287 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 276 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain F residue 101 ARG Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 1135 GLN Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 660 GLU Chi-restraints excluded: chain G residue 1224 ARG Chi-restraints excluded: chain G residue 1275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 chunk 197 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 98 optimal weight: 0.3980 chunk 232 optimal weight: 4.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 193 ASN F 834 GLN F1111 GLN G 186 GLN G 424 ASN G 708 ASN G1098 GLN G1268 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 26375 Z= 0.350 Angle : 0.646 12.100 35855 Z= 0.343 Chirality : 0.047 0.184 4094 Planarity : 0.005 0.076 4514 Dihedral : 11.993 73.963 4074 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 1.70 % Allowed : 7.82 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.16 (0.14), residues: 3150 helix: 0.61 (0.15), residues: 1126 sheet: 0.04 (0.25), residues: 392 loop : -0.12 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 807 HIS 0.011 0.002 HIS F1070 PHE 0.023 0.002 PHE F1323 TYR 0.021 0.002 TYR G 723 ARG 0.013 0.001 ARG F1033 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 288 time to evaluate : 2.422 Fit side-chains revert: symmetry clash REVERT: E 170 ARG cc_start: 0.5694 (OUTLIER) cc_final: 0.4710 (mtm110) REVERT: F 101 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6371 (ptm160) REVERT: F 187 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: F 361 SER cc_start: 0.7582 (OUTLIER) cc_final: 0.7183 (p) REVERT: F 957 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7799 (tppt) REVERT: F 1029 LEU cc_start: 0.7455 (tp) cc_final: 0.7131 (tp) REVERT: F 1135 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: F 1137 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: G 399 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7747 (mtpp) REVERT: G 562 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: G 712 GLN cc_start: 0.7142 (mp10) cc_final: 0.6837 (mp10) REVERT: G 846 GLU cc_start: 0.7411 (pt0) cc_final: 0.7059 (pt0) REVERT: G 983 LYS cc_start: 0.6745 (mppt) cc_final: 0.6391 (mppt) REVERT: G 1224 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6856 (mtm-85) REVERT: G 1276 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6632 (tt0) REVERT: G 1368 ASP cc_start: 0.7573 (t0) cc_final: 0.7330 (m-30) outliers start: 46 outliers final: 14 residues processed: 313 average time/residue: 1.8706 time to fit residues: 659.5685 Evaluate side-chains 303 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 280 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain F residue 101 ARG Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 361 SER Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 890 LYS Chi-restraints excluded: chain F residue 1135 GLN Chi-restraints excluded: chain F residue 1137 GLU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 666 GLU Chi-restraints excluded: chain G residue 952 VAL Chi-restraints excluded: chain G residue 1175 LEU Chi-restraints excluded: chain G residue 1224 ARG Chi-restraints excluded: chain G residue 1276 GLU Chi-restraints excluded: chain G residue 1344 LEU Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 0.7980 chunk 218 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 291 optimal weight: 0.9980 chunk 308 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 276 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 193 ASN F 490 GLN G 186 GLN G 277 ASN G 667 GLN G 708 ASN G1268 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26375 Z= 0.244 Angle : 0.567 10.140 35855 Z= 0.302 Chirality : 0.044 0.158 4094 Planarity : 0.005 0.077 4514 Dihedral : 11.813 73.887 4074 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.45 % Allowed : 9.60 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3150 helix: 0.71 (0.15), residues: 1125 sheet: 0.15 (0.25), residues: 378 loop : -0.11 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 807 HIS 0.008 0.001 HIS E 66 PHE 0.019 0.002 PHE F1323 TYR 0.017 0.002 TYR G 723 ARG 0.015 0.000 ARG F1033 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 293 time to evaluate : 3.032 Fit side-chains revert: symmetry clash REVERT: E 170 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.5432 (pmt170) REVERT: F 20 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: F 957 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7777 (tppt) REVERT: F 1135 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: G 192 MET cc_start: 0.7445 (ptm) cc_final: 0.6839 (ppp) REVERT: G 196 GLN cc_start: 0.7259 (pt0) cc_final: 0.6713 (mm-40) REVERT: G 201 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7398 (mp) REVERT: G 222 LYS cc_start: 0.7814 (tppt) cc_final: 0.7583 (tppt) REVERT: G 225 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6634 (mm-30) REVERT: G 399 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7743 (mtpp) REVERT: G 562 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: G 660 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: G 712 GLN cc_start: 0.7116 (mp10) cc_final: 0.6775 (mp10) REVERT: G 846 GLU cc_start: 0.7370 (pt0) cc_final: 0.6993 (pt0) REVERT: G 982 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6449 (tp) REVERT: G 983 LYS cc_start: 0.6820 (mppt) cc_final: 0.6560 (mptt) REVERT: G 1188 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.4225 (tp30) REVERT: G 1212 ASP cc_start: 0.6568 (m-30) cc_final: 0.6184 (t70) REVERT: G 1224 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.6908 (mtm-85) REVERT: G 1276 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6621 (tm-30) REVERT: G 1368 ASP cc_start: 0.7550 (t0) cc_final: 0.7327 (m-30) outliers start: 39 outliers final: 16 residues processed: 313 average time/residue: 1.8556 time to fit residues: 653.4992 Evaluate side-chains 301 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 275 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 95 LYS Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 890 LYS Chi-restraints excluded: chain F residue 1135 GLN Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 430 HIS Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 660 GLU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 952 VAL Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1188 GLU Chi-restraints excluded: chain G residue 1224 ARG Chi-restraints excluded: chain G residue 1276 GLU Chi-restraints excluded: chain G residue 1344 LEU Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 229 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 157 optimal weight: 0.0980 chunk 276 optimal weight: 10.0000 chunk 77 optimal weight: 0.0970 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 490 GLN G 186 GLN G 667 GLN G 708 ASN G1268 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26375 Z= 0.189 Angle : 0.537 16.761 35855 Z= 0.282 Chirality : 0.043 0.154 4094 Planarity : 0.004 0.074 4514 Dihedral : 11.671 73.802 4074 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.33 % Allowed : 10.12 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3150 helix: 0.82 (0.16), residues: 1131 sheet: 0.22 (0.25), residues: 373 loop : -0.07 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 807 HIS 0.008 0.001 HIS E 66 PHE 0.015 0.001 PHE F1323 TYR 0.015 0.001 TYR G 723 ARG 0.016 0.000 ARG F1033 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 283 time to evaluate : 2.511 Fit side-chains revert: symmetry clash REVERT: E 170 ARG cc_start: 0.5697 (OUTLIER) cc_final: 0.4712 (mtm110) REVERT: F 101 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6227 (ptm160) REVERT: F 957 LYS cc_start: 0.7836 (ttmm) cc_final: 0.7581 (tppt) REVERT: F 1135 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: G 60 ARG cc_start: 0.7074 (ptp-170) cc_final: 0.6604 (ptp90) REVERT: G 192 MET cc_start: 0.7269 (ptm) cc_final: 0.6899 (ppp) REVERT: G 196 GLN cc_start: 0.7278 (pt0) cc_final: 0.6753 (mm-40) REVERT: G 225 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6566 (mm-30) REVERT: G 270 ARG cc_start: 0.7111 (mtp85) cc_final: 0.6694 (mtm180) REVERT: G 399 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7743 (mtpp) REVERT: G 562 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: G 660 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: G 712 GLN cc_start: 0.7168 (mp10) cc_final: 0.6786 (mp10) REVERT: G 846 GLU cc_start: 0.7339 (pt0) cc_final: 0.7066 (pt0) REVERT: G 982 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6488 (tp) REVERT: G 983 LYS cc_start: 0.6879 (mppt) cc_final: 0.6631 (mptt) REVERT: G 993 GLU cc_start: 0.6582 (mp0) cc_final: 0.6068 (mm-30) REVERT: G 1188 GLU cc_start: 0.5060 (OUTLIER) cc_final: 0.4224 (tp30) REVERT: G 1212 ASP cc_start: 0.6565 (m-30) cc_final: 0.6170 (t70) REVERT: G 1224 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6889 (mtm-85) REVERT: G 1276 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6649 (tm-30) REVERT: G 1368 ASP cc_start: 0.7579 (t0) cc_final: 0.7287 (m-30) outliers start: 36 outliers final: 13 residues processed: 303 average time/residue: 1.8332 time to fit residues: 625.7512 Evaluate side-chains 291 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 269 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain F residue 101 ARG Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 890 LYS Chi-restraints excluded: chain F residue 943 LYS Chi-restraints excluded: chain F residue 1135 GLN Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 430 HIS Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 660 GLU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 952 VAL Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1188 GLU Chi-restraints excluded: chain G residue 1224 ARG Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1276 GLU Chi-restraints excluded: chain G residue 1344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 0.3980 chunk 277 optimal weight: 0.0370 chunk 60 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 308 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 490 GLN F 628 HIS F 834 GLN G 186 GLN G 274 ASN G 708 ASN G1268 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26375 Z= 0.161 Angle : 0.506 13.309 35855 Z= 0.266 Chirality : 0.042 0.150 4094 Planarity : 0.004 0.070 4514 Dihedral : 11.523 73.693 4074 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.89 % Allowed : 10.79 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3150 helix: 0.98 (0.16), residues: 1122 sheet: 0.31 (0.25), residues: 372 loop : 0.01 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 807 HIS 0.009 0.001 HIS E 66 PHE 0.012 0.001 PHE F1323 TYR 0.013 0.001 TYR G 723 ARG 0.018 0.000 ARG F1033 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 280 time to evaluate : 2.839 Fit side-chains revert: symmetry clash REVERT: E 170 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.4745 (mtm180) REVERT: F 187 GLU cc_start: 0.8077 (pt0) cc_final: 0.7776 (pm20) REVERT: F 490 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: F 957 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7623 (tppt) REVERT: F 1135 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: G 60 ARG cc_start: 0.7074 (ptp-170) cc_final: 0.6599 (ptp90) REVERT: G 140 TYR cc_start: 0.6981 (m-80) cc_final: 0.6552 (m-80) REVERT: G 192 MET cc_start: 0.7182 (ptm) cc_final: 0.6915 (ppp) REVERT: G 195 GLU cc_start: 0.6648 (mp0) cc_final: 0.6395 (mp0) REVERT: G 213 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7454 (mmmm) REVERT: G 225 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6617 (mm-30) REVERT: G 270 ARG cc_start: 0.7088 (mtp85) cc_final: 0.6877 (mtp85) REVERT: G 304 ASP cc_start: 0.7630 (p0) cc_final: 0.7153 (m-30) REVERT: G 399 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7705 (mtpp) REVERT: G 562 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: G 660 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: G 712 GLN cc_start: 0.7102 (mp10) cc_final: 0.6709 (mp10) REVERT: G 846 GLU cc_start: 0.7340 (pt0) cc_final: 0.7066 (pt0) REVERT: G 983 LYS cc_start: 0.6888 (mppt) cc_final: 0.6540 (mppt) REVERT: G 1188 GLU cc_start: 0.5046 (OUTLIER) cc_final: 0.4204 (tp30) REVERT: G 1212 ASP cc_start: 0.6533 (m-30) cc_final: 0.6147 (t70) REVERT: G 1276 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: G 1368 ASP cc_start: 0.7544 (t0) cc_final: 0.7299 (m-30) outliers start: 24 outliers final: 9 residues processed: 294 average time/residue: 1.8471 time to fit residues: 610.8991 Evaluate side-chains 287 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 271 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 490 GLN Chi-restraints excluded: chain F residue 943 LYS Chi-restraints excluded: chain F residue 1135 GLN Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 660 GLU Chi-restraints excluded: chain G residue 710 ASP Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 952 VAL Chi-restraints excluded: chain G residue 1188 GLU Chi-restraints excluded: chain G residue 1276 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 259 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 307 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 490 GLN F 834 GLN G 186 GLN G 708 ASN ** G 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1268 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 26375 Z= 0.410 Angle : 0.678 12.095 35855 Z= 0.358 Chirality : 0.048 0.166 4094 Planarity : 0.006 0.075 4514 Dihedral : 12.020 74.013 4074 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.41 % Allowed : 11.08 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.14 (0.15), residues: 3150 helix: 0.59 (0.15), residues: 1125 sheet: -0.01 (0.24), residues: 419 loop : -0.11 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 807 HIS 0.009 0.002 HIS F1070 PHE 0.024 0.003 PHE F1164 TYR 0.022 0.002 TYR G 723 ARG 0.016 0.001 ARG F1033 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 272 time to evaluate : 2.972 Fit side-chains REVERT: E 170 ARG cc_start: 0.5642 (OUTLIER) cc_final: 0.5274 (pmt170) REVERT: F 101 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6295 (ptm160) REVERT: F 490 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: F 1135 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: F 1137 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: G 192 MET cc_start: 0.7244 (ptm) cc_final: 0.6914 (ppp) REVERT: G 201 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7447 (mp) REVERT: G 213 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7435 (mmmm) REVERT: G 225 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6678 (mm-30) REVERT: G 562 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: G 712 GLN cc_start: 0.7289 (mp10) cc_final: 0.6983 (mm110) REVERT: G 846 GLU cc_start: 0.7402 (pt0) cc_final: 0.7017 (pt0) REVERT: G 993 GLU cc_start: 0.6614 (mp0) cc_final: 0.6087 (mm-30) REVERT: G 1188 GLU cc_start: 0.4979 (OUTLIER) cc_final: 0.3904 (tp30) REVERT: G 1224 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7085 (mtm-85) REVERT: G 1276 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6569 (tt0) REVERT: G 1368 ASP cc_start: 0.7645 (t0) cc_final: 0.7362 (m-30) outliers start: 38 outliers final: 15 residues processed: 294 average time/residue: 1.8873 time to fit residues: 624.0518 Evaluate side-chains 284 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain F residue 101 ARG Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 490 GLN Chi-restraints excluded: chain F residue 890 LYS Chi-restraints excluded: chain F residue 943 LYS Chi-restraints excluded: chain F residue 1135 GLN Chi-restraints excluded: chain F residue 1137 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 430 HIS Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 666 GLU Chi-restraints excluded: chain G residue 710 ASP Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 952 VAL Chi-restraints excluded: chain G residue 1188 GLU Chi-restraints excluded: chain G residue 1224 ARG Chi-restraints excluded: chain G residue 1276 GLU Chi-restraints excluded: chain G residue 1344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 60 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 490 GLN F 628 HIS G 186 GLN G 667 GLN G 708 ASN G1268 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26375 Z= 0.170 Angle : 0.526 11.781 35855 Z= 0.276 Chirality : 0.042 0.151 4094 Planarity : 0.004 0.076 4514 Dihedral : 11.636 73.715 4074 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.93 % Allowed : 11.86 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3150 helix: 0.87 (0.16), residues: 1126 sheet: 0.25 (0.25), residues: 372 loop : -0.06 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 807 HIS 0.007 0.001 HIS E 66 PHE 0.013 0.001 PHE F1323 TYR 0.013 0.001 TYR G 631 ARG 0.018 0.000 ARG F1033 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 271 time to evaluate : 3.014 Fit side-chains REVERT: E 170 ARG cc_start: 0.5610 (OUTLIER) cc_final: 0.5216 (pmt170) REVERT: F 490 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: F 940 GLU cc_start: 0.6340 (tp30) cc_final: 0.6012 (tp30) REVERT: F 1135 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: G 192 MET cc_start: 0.7190 (ptm) cc_final: 0.6952 (ppp) REVERT: G 213 LYS cc_start: 0.7650 (mmtt) cc_final: 0.7382 (mmmm) REVERT: G 225 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6649 (mm-30) REVERT: G 270 ARG cc_start: 0.6954 (mtp85) cc_final: 0.6750 (mtm180) REVERT: G 304 ASP cc_start: 0.7452 (p0) cc_final: 0.7158 (m-30) REVERT: G 562 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: G 712 GLN cc_start: 0.7164 (mp10) cc_final: 0.6778 (mp10) REVERT: G 846 GLU cc_start: 0.7349 (pt0) cc_final: 0.7084 (pt0) REVERT: G 983 LYS cc_start: 0.6924 (mppt) cc_final: 0.6475 (mppt) REVERT: G 993 GLU cc_start: 0.6587 (mp0) cc_final: 0.6105 (mm-30) REVERT: G 1188 GLU cc_start: 0.5002 (OUTLIER) cc_final: 0.4004 (tp30) REVERT: G 1212 ASP cc_start: 0.6523 (m-30) cc_final: 0.6243 (t70) REVERT: G 1276 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: G 1368 ASP cc_start: 0.7540 (t0) cc_final: 0.7312 (m-30) outliers start: 25 outliers final: 9 residues processed: 284 average time/residue: 1.8477 time to fit residues: 592.8271 Evaluate side-chains 272 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 257 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 490 GLN Chi-restraints excluded: chain F residue 890 LYS Chi-restraints excluded: chain F residue 1135 GLN Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 710 ASP Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 952 VAL Chi-restraints excluded: chain G residue 1188 GLU Chi-restraints excluded: chain G residue 1276 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 279 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 286 optimal weight: 0.0670 chunk 172 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 258 optimal weight: 0.0010 chunk 270 optimal weight: 7.9990 chunk 285 optimal weight: 0.9990 overall best weight: 0.5928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 ASN F 46 GLN F 387 ASN F 490 GLN G 186 GLN G 667 GLN G 708 ASN G1268 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26375 Z= 0.146 Angle : 0.502 12.094 35855 Z= 0.263 Chirality : 0.041 0.148 4094 Planarity : 0.004 0.081 4514 Dihedral : 11.470 73.630 4074 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.82 % Allowed : 12.05 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3150 helix: 1.12 (0.16), residues: 1106 sheet: 0.29 (0.25), residues: 384 loop : 0.06 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 807 HIS 0.008 0.001 HIS E 66 PHE 0.011 0.001 PHE G1319 TYR 0.012 0.001 TYR G 723 ARG 0.019 0.000 ARG F1033 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 269 time to evaluate : 2.971 Fit side-chains REVERT: E 170 ARG cc_start: 0.5464 (OUTLIER) cc_final: 0.5149 (pmt170) REVERT: F 201 ARG cc_start: 0.7519 (mmt90) cc_final: 0.7273 (mmm-85) REVERT: F 492 MET cc_start: 0.6820 (mtm) cc_final: 0.6571 (mpp) REVERT: F 940 GLU cc_start: 0.6326 (tp30) cc_final: 0.6002 (tp30) REVERT: F 1135 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: G 60 ARG cc_start: 0.7039 (ptp-170) cc_final: 0.6452 (ptp90) REVERT: G 192 MET cc_start: 0.7285 (ptm) cc_final: 0.6918 (ppp) REVERT: G 213 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7372 (mmmm) REVERT: G 225 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6599 (mm-30) REVERT: G 304 ASP cc_start: 0.7420 (p0) cc_final: 0.7111 (m-30) REVERT: G 497 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8483 (mm-30) REVERT: G 562 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: G 712 GLN cc_start: 0.7141 (mp10) cc_final: 0.6733 (mp10) REVERT: G 846 GLU cc_start: 0.7284 (pt0) cc_final: 0.7019 (pt0) REVERT: G 983 LYS cc_start: 0.6926 (mppt) cc_final: 0.6514 (mppt) REVERT: G 993 GLU cc_start: 0.6562 (mp0) cc_final: 0.6089 (mm-30) REVERT: G 1188 GLU cc_start: 0.4990 (OUTLIER) cc_final: 0.4007 (tp30) REVERT: G 1212 ASP cc_start: 0.6496 (m-30) cc_final: 0.6267 (t70) REVERT: G 1276 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6596 (tm-30) outliers start: 22 outliers final: 9 residues processed: 284 average time/residue: 1.7764 time to fit residues: 569.6182 Evaluate side-chains 274 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 260 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 490 GLN Chi-restraints excluded: chain F residue 890 LYS Chi-restraints excluded: chain F residue 1135 GLN Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 710 ASP Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 952 VAL Chi-restraints excluded: chain G residue 1188 GLU Chi-restraints excluded: chain G residue 1276 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 10.0000 chunk 302 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 317 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 chunk 253 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 387 ASN ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN G 708 ASN G1268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26375 Z= 0.233 Angle : 0.568 12.242 35855 Z= 0.299 Chirality : 0.043 0.158 4094 Planarity : 0.005 0.083 4514 Dihedral : 11.657 73.702 4074 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.78 % Allowed : 12.12 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3150 helix: 0.95 (0.16), residues: 1116 sheet: 0.22 (0.25), residues: 392 loop : 0.05 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 807 HIS 0.008 0.001 HIS E 66 PHE 0.018 0.002 PHE F 35 TYR 0.019 0.002 TYR G 723 ARG 0.019 0.000 ARG F1033 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 258 time to evaluate : 2.868 Fit side-chains REVERT: E 170 ARG cc_start: 0.5436 (OUTLIER) cc_final: 0.5117 (pmt170) REVERT: F 201 ARG cc_start: 0.7568 (mmt90) cc_final: 0.7268 (mmm-85) REVERT: F 940 GLU cc_start: 0.6329 (tp30) cc_final: 0.6026 (tp30) REVERT: F 1135 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: G 68 TYR cc_start: 0.7340 (m-80) cc_final: 0.6935 (m-80) REVERT: G 192 MET cc_start: 0.7340 (ptm) cc_final: 0.6941 (ppp) REVERT: G 213 LYS cc_start: 0.7658 (mmtt) cc_final: 0.7364 (mmmm) REVERT: G 225 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6694 (mm-30) REVERT: G 304 ASP cc_start: 0.7522 (p0) cc_final: 0.7171 (m-30) REVERT: G 562 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: G 712 GLN cc_start: 0.7187 (mp10) cc_final: 0.6903 (mm110) REVERT: G 846 GLU cc_start: 0.7306 (pt0) cc_final: 0.6955 (pt0) REVERT: G 993 GLU cc_start: 0.6585 (mp0) cc_final: 0.6089 (mm-30) REVERT: G 1188 GLU cc_start: 0.4951 (OUTLIER) cc_final: 0.3922 (tp30) REVERT: G 1224 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6999 (mtm-85) REVERT: G 1276 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6629 (tm-30) outliers start: 20 outliers final: 11 residues processed: 271 average time/residue: 1.9273 time to fit residues: 589.2861 Evaluate side-chains 272 residues out of total 2689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 890 LYS Chi-restraints excluded: chain F residue 1135 GLN Chi-restraints excluded: chain G residue 158 GLN Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 430 HIS Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 505 ASP Chi-restraints excluded: chain G residue 562 GLU Chi-restraints excluded: chain G residue 710 ASP Chi-restraints excluded: chain G residue 952 VAL Chi-restraints excluded: chain G residue 1188 GLU Chi-restraints excluded: chain G residue 1224 ARG Chi-restraints excluded: chain G residue 1276 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 0.9990 chunk 269 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 70 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 387 ASN F 490 GLN G 186 GLN G 667 GLN G 708 ASN G1268 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.164341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106394 restraints weight = 59160.900| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.29 r_work: 0.3095 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26375 Z= 0.215 Angle : 0.554 12.293 35855 Z= 0.292 Chirality : 0.043 0.155 4094 Planarity : 0.004 0.084 4514 Dihedral : 11.642 73.678 4074 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.78 % Allowed : 12.19 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3150 helix: 0.89 (0.16), residues: 1117 sheet: 0.21 (0.25), residues: 387 loop : 0.03 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 807 HIS 0.008 0.001 HIS E 66 PHE 0.016 0.002 PHE F 35 TYR 0.017 0.002 TYR G 723 ARG 0.019 0.000 ARG F1033 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11973.67 seconds wall clock time: 212 minutes 4.85 seconds (12724.85 seconds total)