Starting phenix.real_space_refine on Sun May 25 05:58:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fvr_29491/05_2025/8fvr_29491.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fvr_29491/05_2025/8fvr_29491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fvr_29491/05_2025/8fvr_29491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fvr_29491/05_2025/8fvr_29491.map" model { file = "/net/cci-nas-00/data/ceres_data/8fvr_29491/05_2025/8fvr_29491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fvr_29491/05_2025/8fvr_29491.cif" } resolution = 2.42 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= 0.077 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 107 5.16 5 C 16047 2.51 5 N 4581 2.21 5 O 5254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26040 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: 10437 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1319, 10400 Classifications: {'peptide': 1319} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 1319, 10400 Classifications: {'peptide': 1319} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 10523 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: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} 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 14309 SG CYS G 70 114.191 95.607 90.676 1.00116.05 S ATOM 14323 SG CYS G 72 113.603 98.892 92.155 1.00109.53 S ATOM 14431 SG CYS G 85 115.567 97.164 93.693 1.00108.56 S ATOM 14455 SG CYS G 88 112.056 97.117 94.336 1.00117.41 S ATOM 20143 SG CYS G 814 88.007 35.246 87.039 1.00 58.06 S ATOM 20708 SG CYS G 888 86.532 38.503 87.163 1.00 56.22 S ATOM 20759 SG CYS G 895 87.183 37.039 83.913 1.00 62.07 S ATOM 20780 SG CYS G 898 84.307 35.863 85.230 1.00 70.08 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O HOH H 103 " occ=0.67 Time building chain proxies: 20.02, per 1000 atoms: 0.77 Number of scatterers: 26040 At special positions: 0 Unit cell: (130.35, 158.4, 164.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 107 16.00 P 48 15.00 Mg 1 11.99 O 5254 8.00 N 4581 7.00 C 16047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.26 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G1501 " pdb="ZN ZN G1501 " - pdb=" SG CYS G 85 " pdb="ZN ZN G1501 " - pdb=" SG CYS G 88 " pdb="ZN ZN G1501 " - pdb=" SG CYS G 70 " pdb="ZN ZN G1501 " - pdb=" SG CYS G 72 " pdb=" ZN G1502 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 898 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 814 " pdb="ZN ZN G1502 " - pdb=" SG CYS G 895 " pdb="ZN ZN G1502 " - 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... Secondary structure from input PDB file: 117 helices and 47 sheets defined 40.4% alpha, 17.9% beta 20 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 10.50 Creating SS restraints... Processing helix chain 'D' and resid 34 through 51 removed outlier: 4.068A pdb=" N MET D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 212 through 233 removed outlier: 4.348A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 50 Processing helix chain 'E' and resid 77 through 87 removed outlier: 3.595A pdb=" N GLY E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 212 through 228 removed outlier: 3.541A pdb=" N LEU E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 10 removed outlier: 3.559A pdb=" N ARG F 10 " --> pdb=" O GLU F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 48 through 57 removed outlier: 3.583A pdb=" N VAL F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 89 Processing helix chain 'F' and resid 206 through 213 removed outlier: 3.569A pdb=" N LEU F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 225 Processing helix chain 'F' and resid 242 through 247 removed outlier: 4.303A pdb=" N LEU F 246 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG F 247 " --> pdb=" O PRO F 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 242 through 247' Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 289 through 294 removed outlier: 3.857A pdb=" N GLY F 294 " --> pdb=" O TYR F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 327 Processing helix chain 'F' and resid 345 through 354 Processing helix chain 'F' and resid 358 through 371 Processing helix chain 'F' and resid 377 through 390 removed outlier: 4.014A pdb=" N PHE F 389 " --> pdb=" O PHE F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 409 Processing helix chain 'F' and resid 421 through 437 Processing helix chain 'F' and resid 455 through 481 removed outlier: 3.721A pdb=" N ALA F 474 " --> pdb=" O ARG F 470 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU F 477 " --> pdb=" O ARG F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 493 removed outlier: 3.958A pdb=" N MET F 492 " --> pdb=" O MET F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 509 removed outlier: 3.580A pdb=" N SER F 509 " --> pdb=" O PHE F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 528 Processing helix chain 'F' and resid 544 through 549 removed outlier: 3.649A pdb=" N ARG F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 555 Processing helix chain 'F' and resid 608 through 612 removed outlier: 3.601A pdb=" N GLY F 612 " --> pdb=" O ALA F 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 608 through 612' Processing helix chain 'F' and resid 662 through 667 Processing helix chain 'F' and resid 670 through 674 Processing helix chain 'F' and resid 675 through 687 removed outlier: 4.026A pdb=" N ARG F 687 " --> pdb=" O ALA F 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 713 removed outlier: 4.059A pdb=" N GLY F 713 " --> pdb=" O ALA F 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 741 removed outlier: 3.649A pdb=" N MET F 741 " --> pdb=" O GLU F 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 738 through 741' Processing helix chain 'F' and resid 811 through 815 removed outlier: 3.862A pdb=" N ASP F 814 " --> pdb=" O ASN F 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 825 Processing helix chain 'F' and resid 859 through 863 Processing helix chain 'F' and resid 942 through 980 removed outlier: 3.544A pdb=" N GLU F 963 " --> pdb=" O ASP F 959 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU F 964 " --> pdb=" O LEU F 960 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 992 removed outlier: 3.531A pdb=" N LEU F 989 " --> pdb=" O GLU F 985 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP F 990 " --> pdb=" O ALA F 986 " (cutoff:3.500A) Processing helix chain 'F' and resid 993 through 1000 removed outlier: 3.889A pdb=" N TRP F 997 " --> pdb=" O PRO F 993 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU F 998 " --> pdb=" O ARG F 994 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU F 999 " --> pdb=" O ASP F 995 " (cutoff:3.500A) Processing helix chain 'F' and resid 1005 through 1010 removed outlier: 4.248A pdb=" N GLN F1010 " --> pdb=" O GLU F1006 " (cutoff:3.500A) Processing helix chain 'F' and resid 1010 through 1023 removed outlier: 3.720A pdb=" N GLU F1016 " --> pdb=" O GLU F1012 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN F1017 " --> pdb=" O GLN F1013 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR F1018 " --> pdb=" O LEU F1014 " (cutoff:3.500A) Processing helix chain 'F' and resid 1026 through 1038 removed outlier: 4.234A pdb=" N GLU F1030 " --> pdb=" O GLU F1026 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA F1031 " --> pdb=" O LYS F1027 " (cutoff:3.500A) Processing helix chain 'F' and resid 1081 through 1085 Processing helix chain 'F' and resid 1099 through 1103 Processing helix chain 'F' and resid 1109 through 1134 Processing helix chain 'F' and resid 1137 through 1151 Processing helix chain 'F' and resid 1160 through 1164 Processing helix chain 'F' and resid 1165 through 1177 Processing helix chain 'F' and resid 1191 through 1202 Processing helix chain 'F' and resid 1238 through 1243 Processing helix chain 'F' and resid 1271 through 1282 Processing helix chain 'F' and resid 1283 through 1292 Processing helix chain 'F' and resid 1297 through 1310 Processing helix chain 'F' and resid 1320 through 1333 removed outlier: 3.631A pdb=" N ASN F1324 " --> pdb=" O PRO F1320 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 33 Processing helix chain 'G' and resid 58 through 63 Processing helix chain 'G' and resid 77 through 81 Processing helix chain 'G' and resid 94 through 100 Processing helix chain 'G' and resid 114 through 119 removed outlier: 3.508A pdb=" N SER G 119 " --> pdb=" O TRP G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 131 through 140 Processing helix chain 'G' and resid 161 through 172 Processing helix chain 'G' and resid 180 through 192 removed outlier: 3.874A pdb=" N ALA G 184 " --> pdb=" O MET G 180 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE G 185 " --> pdb=" O GLY G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 207 removed outlier: 3.773A pdb=" N ASN G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 231 removed outlier: 3.543A pdb=" N LEU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 246 through 250 Processing helix chain 'G' and resid 265 through 285 Processing helix chain 'G' and resid 288 through 308 Processing helix chain 'G' and resid 326 through 332 removed outlier: 4.112A pdb=" N ILE G 331 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'G' and resid 370 through 377 Processing helix chain 'G' and resid 377 through 388 Processing helix chain 'G' and resid 393 through 404 Processing helix chain 'G' and resid 405 through 416 Processing helix chain 'G' and resid 430 through 432 No H-bonds generated for 'chain 'G' and resid 430 through 432' Processing helix chain 'G' and resid 450 through 452 No H-bonds generated for 'chain 'G' and resid 450 through 452' Processing helix chain 'G' and resid 453 through 458 Processing helix chain 'G' and resid 473 through 483 Processing helix chain 'G' and resid 485 through 489 Processing helix chain 'G' and resid 504 through 515 Processing helix chain 'G' and resid 529 through 539 Processing helix chain 'G' and resid 574 through 581 removed outlier: 3.768A pdb=" N MET G 581 " --> pdb=" O ALA G 577 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 592 Processing helix chain 'G' and resid 597 through 613 Processing helix chain 'G' and resid 613 through 636 removed outlier: 3.771A pdb=" N GLY G 636 " --> pdb=" O ALA G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 640 through 644 Processing helix chain 'G' and resid 649 through 670 Processing helix chain 'G' and resid 674 through 702 Processing helix chain 'G' and resid 720 through 729 Processing helix chain 'G' and resid 733 through 742 Processing helix chain 'G' and resid 768 through 805 removed outlier: 3.675A pdb=" N HIS G 777 " --> pdb=" O PHE G 773 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY G 778 " --> pdb=" O ILE G 774 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA G 791 " --> pdb=" O ALA G 787 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN G 792 " --> pdb=" O LEU G 788 " (cutoff:3.500A) Processing helix chain 'G' and resid 834 through 840 Processing helix chain 'G' and resid 865 through 875 Processing helix chain 'G' and resid 896 through 900 Processing helix chain 'G' and resid 914 through 925 Processing helix chain 'G' and resid 926 through 930 Processing helix chain 'G' and resid 1068 through 1074 removed outlier: 4.002A pdb=" N ASP G1073 " --> pdb=" O ALA G1069 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU G1074 " --> pdb=" O GLY G1070 " (cutoff:3.500A) Processing helix chain 'G' and resid 1137 through 1146 Processing helix chain 'G' and resid 1216 through 1225 Processing helix chain 'G' and resid 1225 through 1244 removed outlier: 3.723A pdb=" N GLN G1244 " --> pdb=" O VAL G1240 " (cutoff:3.500A) Processing helix chain 'G' and resid 1249 through 1261 removed outlier: 4.181A pdb=" N ILE G1253 " --> pdb=" O ASN G1249 " (cutoff:3.500A) Processing helix chain 'G' and resid 1282 through 1296 Processing helix chain 'G' and resid 1308 through 1315 Processing helix chain 'G' and resid 1318 through 1326 Processing helix chain 'G' and resid 1327 through 1339 Processing helix chain 'G' and resid 1346 through 1353 Processing helix chain 'G' and resid 1359 through 1361 No H-bonds generated for 'chain 'G' and resid 1359 through 1361' Processing helix chain 'G' and resid 1362 through 1373 removed outlier: 3.520A pdb=" N ARG G1373 " --> pdb=" O ARG G1369 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 14 Processing helix chain 'H' and resid 15 through 32 Processing helix chain 'H' and resid 45 through 56 Processing helix chain 'H' and resid 60 through 74 Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 20 removed outlier: 5.062A pdb=" N LEU D 13 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU D 29 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP D 15 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N HIS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP D 199 " --> pdb=" O PRO D 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 97 through 105 removed outlier: 3.518A pdb=" N GLU D 58 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN D 147 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL D 56 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY D 149 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N CYS D 54 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'D' and resid 108 through 111 removed outlier: 6.486A pdb=" N GLY D 108 " --> pdb=" O HIS D 132 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS D 132 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D 110 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'E' and resid 13 through 18 removed outlier: 6.023A pdb=" N HIS E 23 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N THR E 207 " --> pdb=" O HIS E 23 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS E 25 " --> pdb=" O MET E 205 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET E 205 " --> pdb=" O LYS E 25 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N THR E 27 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE E 203 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLU E 29 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU E 201 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 97 through 105 removed outlier: 7.634A pdb=" N SER E 141 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE E 61 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG E 143 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL E 59 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS E 145 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'E' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'E' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.416A pdb=" N LYS F 13 " --> pdb=" O ALA F1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 59 through 60 removed outlier: 6.363A pdb=" N SER F 66 " --> pdb=" O TYR F 105 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR F 105 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU F 68 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL F 103 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TYR F 70 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG F 101 " --> pdb=" O TYR F 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER F 72 " --> pdb=" O LYS F 99 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY F 125 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL F 98 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR F 123 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU F 100 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU F 121 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU F 102 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLU F 119 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE F 104 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE F 117 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'F' and resid 451 through 454 removed outlier: 6.487A pdb=" N SER F 147 " --> pdb=" O SER F 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 154 through 160 removed outlier: 3.590A pdb=" N ASP F 160 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 171 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR F 172 " --> pdb=" O PHE F 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 284 through 285 removed outlier: 3.535A pdb=" N GLU F 240 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE F 229 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 255 through 257 removed outlier: 6.820A pdb=" N ILE F 255 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 296 through 297 removed outlier: 3.696A pdb=" N MET F 315 " --> pdb=" O VAL F 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 580 through 581 removed outlier: 5.370A pdb=" N GLU F 602 " --> pdb=" O LYS F 593 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR F 595 " --> pdb=" O THR F 600 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR F 600 " --> pdb=" O THR F 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'F' and resid 716 through 717 removed outlier: 6.383A pdb=" N ALA F 716 " --> pdb=" O LEU F 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 748 through 752 removed outlier: 6.665A pdb=" N ARG F 731 " --> pdb=" O VAL F 727 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL F 727 " --> pdb=" O ARG F 731 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL F 733 " --> pdb=" O GLN F 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'F' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'F' and resid 1209 through 1210 removed outlier: 7.413A pdb=" N ILE F 816 " --> pdb=" O SER F1077 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE F1079 " --> pdb=" O ILE F 816 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL F 818 " --> pdb=" O ILE F1079 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE F1096 " --> pdb=" O ASN F 799 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG F 801 " --> pdb=" O ILE F1096 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU F1098 " --> pdb=" O ARG F 801 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA F 803 " --> pdb=" O LEU F1098 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR F1226 " --> pdb=" O PHE F 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 830 through 841 removed outlier: 3.866A pdb=" N ASP F 930 " --> pdb=" O TYR F1053 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA F1055 " --> pdb=" O VAL F 928 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL F 928 " --> pdb=" O ALA F1055 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LYS F1057 " --> pdb=" O GLY F 926 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY F 926 " --> pdb=" O LYS F1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'F' and resid 882 through 884 removed outlier: 6.748A pdb=" N LEU F 918 " --> pdb=" O LEU F 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 1244 through 1246 Processing sheet with id=AD3, first strand: chain 'F' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'F' and resid 1335 through 1339 Processing sheet with id=AD5, first strand: chain 'G' and resid 34 through 37 removed outlier: 7.635A pdb=" N HIS G 104 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU G 37 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLU G 106 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N LEU G 107 " --> pdb=" O PRO G 243 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N SER G 109 " --> pdb=" O VAL G 241 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL G 241 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 145 through 146 Processing sheet with id=AD7, first strand: chain 'G' and resid 254 through 255 Processing sheet with id=AD8, first strand: chain 'G' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'G' and resid 703 through 707 Processing sheet with id=AE1, first strand: chain 'G' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'G' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'G' and resid 825 through 827 removed outlier: 6.634A pdb=" N VAL G 825 " --> pdb=" O LYS G 832 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP G 830 " --> pdb=" O GLU G 827 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 848 through 849 removed outlier: 6.908A pdb=" N VAL G 848 " --> pdb=" O LEU G 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 949 through 951 removed outlier: 6.719A pdb=" N ILE G 950 " --> pdb=" O VAL G1017 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN G1019 " --> pdb=" O VAL G1002 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL G1002 " --> pdb=" O ASN G1019 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 957 through 961 removed outlier: 4.235A pdb=" N SER G 961 " --> pdb=" O GLU G 981 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU G 981 " --> pdb=" O SER G 961 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 1098 through 1099 removed outlier: 3.629A pdb=" N GLY G1033 " --> pdb=" O ILE G1115 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 1047 through 1049 removed outlier: 4.007A pdb=" N ALA G1105 " --> pdb=" O VAL G1061 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 1155 through 1156 removed outlier: 6.363A pdb=" N ILE G1155 " --> pdb=" O ILE G1210 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 1186 through 1190 Processing sheet with id=AF2, first strand: chain 'G' and resid 1279 through 1281 removed outlier: 4.252A pdb=" N LYS G1263 " --> pdb=" O ASP G1305 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR G1301 " --> pdb=" O VAL G1267 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 13.99 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4775 1.32 - 1.45: 6191 1.45 - 1.57: 15083 1.57 - 1.69: 96 1.69 - 1.81: 186 Bond restraints: 26331 Sorted by residual: bond pdb=" N PRO G 998 " pdb=" CD PRO G 998 " ideal model delta sigma weight residual 1.473 1.429 0.044 1.40e-02 5.10e+03 9.83e+00 bond pdb=" N VAL G 706 " pdb=" CA VAL G 706 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 9.73e+00 bond pdb=" N VAL G 145 " pdb=" CA VAL G 145 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.59e+00 bond pdb=" N ILE G 707 " pdb=" CA ILE G 707 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.33e+00 bond pdb=" N TYR G 144 " pdb=" CA TYR G 144 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.18e-02 7.18e+03 8.08e+00 ... (remaining 26326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 34653 1.64 - 3.27: 968 3.27 - 4.91: 131 4.91 - 6.55: 30 6.55 - 8.18: 4 Bond angle restraints: 35786 Sorted by residual: angle pdb=" C THR G 705 " pdb=" CA THR G 705 " pdb=" CB THR G 705 " ideal model delta sigma weight residual 109.38 116.93 -7.55 1.80e+00 3.09e-01 1.76e+01 angle pdb=" N ASN F 811 " pdb=" CA ASN F 811 " pdb=" C ASN F 811 " ideal model delta sigma weight residual 112.41 107.13 5.28 1.30e+00 5.92e-01 1.65e+01 angle pdb=" N ARG G 709 " pdb=" CA ARG G 709 " pdb=" C ARG G 709 " ideal model delta sigma weight residual 112.54 107.64 4.90 1.22e+00 6.72e-01 1.61e+01 angle pdb=" N ASN G 153 " pdb=" CA ASN G 153 " pdb=" C ASN G 153 " ideal model delta sigma weight residual 112.72 108.72 4.00 1.14e+00 7.69e-01 1.23e+01 angle pdb=" CA THR G 161 " pdb=" C THR G 161 " pdb=" O THR G 161 " ideal model delta sigma weight residual 121.87 118.03 3.84 1.10e+00 8.26e-01 1.22e+01 ... (remaining 35781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 14594 17.85 - 35.70: 1153 35.70 - 53.55: 263 53.55 - 71.40: 94 71.40 - 89.26: 17 Dihedral angle restraints: 16121 sinusoidal: 7014 harmonic: 9107 Sorted by residual: 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 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LYS G1192 " pdb=" C LYS G1192 " pdb=" N TRP G1193 " pdb=" CA TRP G1193 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA CYS G 70 " pdb=" C CYS G 70 " pdb=" N LEU G 71 " pdb=" CA LEU G 71 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 16118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3024 0.046 - 0.092: 788 0.092 - 0.138: 244 0.138 - 0.184: 32 0.184 - 0.230: 2 Chirality restraints: 4090 Sorted by residual: chirality pdb=" CA PRO G1191 " pdb=" N PRO G1191 " pdb=" C PRO G1191 " pdb=" CB PRO G1191 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LEU G 169 " pdb=" N LEU G 169 " pdb=" C LEU G 169 " pdb=" CB LEU G 169 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CA ILE G 159 " pdb=" N ILE G 159 " pdb=" C ILE G 159 " pdb=" CB ILE G 159 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 4087 not shown) Planarity restraints: 4511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 322 " 0.049 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO G 323 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 323 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 323 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G1152 " -0.043 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO G1153 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO G1153 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G1153 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 378 " 0.041 5.00e-02 4.00e+02 6.10e-02 5.94e+00 pdb=" N PRO G 379 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO G 379 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 379 " 0.034 5.00e-02 4.00e+02 ... (remaining 4508 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 268 2.58 - 3.16: 21327 3.16 - 3.74: 42445 3.74 - 4.32: 60611 4.32 - 4.90: 97073 Nonbonded interactions: 221724 Sorted by model distance: nonbonded pdb=" O3' A C 16 " pdb="MG MG G1503 " model vdw 2.002 2.170 nonbonded pdb="MG MG G1503 " pdb=" O HOH G1601 " model vdw 2.068 2.170 nonbonded pdb=" OD1 ASP G 460 " pdb="MG MG G1503 " model vdw 2.195 2.170 nonbonded pdb=" OD1 ASP G 462 " pdb="MG MG G1503 " model vdw 2.199 2.170 nonbonded pdb=" OD1 ASP G 464 " pdb="MG MG G1503 " model vdw 2.200 2.170 ... (remaining 221719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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=0.35 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 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: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 81.870 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.150 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:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26339 Z= 0.190 Angle : 0.727 43.432 35798 Z= 0.373 Chirality : 0.046 0.230 4090 Planarity : 0.005 0.075 4511 Dihedral : 14.459 89.256 10267 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.07 % Allowed : 0.63 % Favored : 99.30 % 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: 0.56 (0.15), residues: 3150 helix: 1.14 (0.16), residues: 1103 sheet: 0.24 (0.25), residues: 411 loop : -0.04 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G1193 HIS 0.005 0.001 HIS F1070 PHE 0.013 0.002 PHE F1164 TYR 0.015 0.001 TYR G1186 ARG 0.007 0.001 ARG G1148 Details of bonding type rmsd hydrogen bonds : bond 0.14232 ( 1138) hydrogen bonds : angle 6.27896 ( 3117) metal coordination : bond 0.02706 ( 8) metal coordination : angle 18.59381 ( 12) covalent geometry : bond 0.00342 (26331) covalent geometry : angle 0.64262 (35786) *********************** 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 421 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 419 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7237 (mt-10) REVERT: F 69 GLN cc_start: 0.8174 (mt0) cc_final: 0.7892 (mt0) REVERT: F 83 GLN cc_start: 0.7906 (mp10) cc_final: 0.7689 (mp10) REVERT: F 195 PHE cc_start: 0.8442 (m-80) cc_final: 0.8196 (m-80) REVERT: F 299 LYS cc_start: 0.6884 (ttpt) cc_final: 0.6181 (ttpt) REVERT: F 367 TYR cc_start: 0.7121 (t80) cc_final: 0.6796 (t80) REVERT: F 376 PRO cc_start: 0.7567 (Cg_endo) cc_final: 0.7022 (Cg_exo) REVERT: F 943 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7797 (mtpp) REVERT: G 40 LYS cc_start: 0.8183 (mttt) cc_final: 0.7796 (ttmt) REVERT: G 87 LYS cc_start: 0.6740 (tttp) cc_final: 0.6249 (tptt) REVERT: G 158 GLN cc_start: 0.7021 (tt0) cc_final: 0.6648 (tt0) REVERT: G 196 GLN cc_start: 0.7732 (tt0) cc_final: 0.7375 (tm-30) REVERT: G 204 GLU cc_start: 0.6288 (tt0) cc_final: 0.5696 (mt-10) REVERT: G 371 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7939 (mtmm) REVERT: G 399 LYS cc_start: 0.8253 (mttt) cc_final: 0.8048 (mtpm) REVERT: G 668 PHE cc_start: 0.7510 (t80) cc_final: 0.6928 (t80) REVERT: G 871 LEU cc_start: 0.7521 (mt) cc_final: 0.7314 (tp) REVERT: G 875 ASN cc_start: 0.7487 (m110) cc_final: 0.7186 (m110) REVERT: G 1205 GLU cc_start: 0.7316 (tt0) cc_final: 0.7055 (tm-30) REVERT: H 8 ASP cc_start: 0.8114 (m-30) cc_final: 0.7854 (m-30) REVERT: H 62 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7234 (tm-30) outliers start: 2 outliers final: 0 residues processed: 419 average time/residue: 1.8475 time to fit residues: 868.7022 Evaluate side-chains 277 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 2.810 ------------------------------------------------------------------------------- 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: 8.9990 chunk 241 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 289 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN F 618 GLN F 824 GLN F 834 GLN F1220 GLN F1336 ASN ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 708 ASN G 968 ASN G1019 ASN H 15 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.089746 restraints weight = 52025.933| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.03 r_work: 0.2929 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 26339 Z= 0.353 Angle : 0.758 11.916 35798 Z= 0.401 Chirality : 0.053 0.203 4090 Planarity : 0.006 0.116 4511 Dihedral : 11.893 73.965 4062 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.11 % Allowed : 8.31 % Favored : 89.58 % 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: 0.34 (0.14), residues: 3150 helix: 0.83 (0.15), residues: 1139 sheet: 0.05 (0.24), residues: 390 loop : -0.05 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 868 HIS 0.011 0.002 HIS F 526 PHE 0.021 0.003 PHE G 116 TYR 0.026 0.003 TYR G 140 ARG 0.010 0.001 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.06062 ( 1138) hydrogen bonds : angle 5.41729 ( 3117) metal coordination : bond 0.01332 ( 8) metal coordination : angle 5.97460 ( 12) covalent geometry : bond 0.00839 (26331) covalent geometry : angle 0.75069 (35786) *********************** 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 355 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 298 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7880 (mt-10) REVERT: E 72 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7258 (mp0) REVERT: E 125 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8096 (ptmm) REVERT: F 284 LEU cc_start: 0.5743 (mm) cc_final: 0.5329 (mm) REVERT: F 299 LYS cc_start: 0.6499 (ttpt) cc_final: 0.6205 (ttpt) REVERT: F 339 ASN cc_start: 0.7549 (m-40) cc_final: 0.7302 (m-40) REVERT: F 490 GLN cc_start: 0.7507 (tp40) cc_final: 0.7237 (mm-40) REVERT: F 738 GLU cc_start: 0.8018 (mp0) cc_final: 0.7693 (mp0) REVERT: F 943 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7980 (mtpp) REVERT: F 963 GLU cc_start: 0.6798 (mp0) cc_final: 0.6375 (mp0) REVERT: G 40 LYS cc_start: 0.8368 (mttt) cc_final: 0.8097 (ttmt) REVERT: G 42 GLU cc_start: 0.6017 (pm20) cc_final: 0.5772 (tm-30) REVERT: G 87 LYS cc_start: 0.6757 (tttp) cc_final: 0.6212 (tptt) REVERT: G 134 ASP cc_start: 0.8030 (m-30) cc_final: 0.7807 (m-30) REVERT: G 157 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: G 158 GLN cc_start: 0.7422 (tt0) cc_final: 0.7190 (tt0) REVERT: G 202 ARG cc_start: 0.7490 (ttt90) cc_final: 0.7196 (ttt90) REVERT: G 204 GLU cc_start: 0.6513 (tt0) cc_final: 0.5815 (mt-10) REVERT: G 290 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6974 (tp) REVERT: G 320 ASN cc_start: 0.7112 (t0) cc_final: 0.6749 (t0) REVERT: G 371 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8161 (mtmm) REVERT: G 860 ARG cc_start: 0.7122 (tmm160) cc_final: 0.6914 (ttp80) REVERT: G 1205 GLU cc_start: 0.7596 (tt0) cc_final: 0.7308 (tt0) outliers start: 57 outliers final: 24 residues processed: 332 average time/residue: 1.7323 time to fit residues: 648.5276 Evaluate side-chains 300 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 273 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 441 GLU Chi-restraints excluded: chain F residue 634 VAL Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 157 GLN Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 298 MET Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 705 THR Chi-restraints excluded: chain G residue 709 ARG Chi-restraints excluded: chain G residue 712 GLN Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 836 ARG Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 891 ASP Chi-restraints excluded: chain G residue 931 THR Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1175 LEU Chi-restraints excluded: chain G residue 1243 LEU Chi-restraints excluded: chain G residue 1371 ARG Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 313 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 236 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN E 127 GLN F 618 GLN F 628 HIS G 80 HIS G 320 ASN ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1019 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.094452 restraints weight = 52289.077| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.08 r_work: 0.3002 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26339 Z= 0.126 Angle : 0.546 9.049 35798 Z= 0.289 Chirality : 0.042 0.160 4090 Planarity : 0.004 0.065 4511 Dihedral : 11.534 73.579 4062 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.59 % Allowed : 10.31 % Favored : 88.10 % 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: 0.69 (0.15), residues: 3150 helix: 1.23 (0.16), residues: 1134 sheet: 0.15 (0.24), residues: 385 loop : 0.09 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G1193 HIS 0.006 0.001 HIS G 104 PHE 0.021 0.001 PHE F 812 TYR 0.019 0.001 TYR G 140 ARG 0.009 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 1138) hydrogen bonds : angle 4.92596 ( 3117) metal coordination : bond 0.00665 ( 8) metal coordination : angle 4.36766 ( 12) covalent geometry : bond 0.00277 (26331) covalent geometry : angle 0.53988 (35786) *********************** 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 336 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7640 (mt-10) REVERT: E 72 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7141 (mp0) REVERT: F 103 VAL cc_start: 0.6824 (t) cc_final: 0.6598 (m) REVERT: F 284 LEU cc_start: 0.5765 (mm) cc_final: 0.5359 (mm) REVERT: F 299 LYS cc_start: 0.6355 (ttpt) cc_final: 0.6055 (ttpt) REVERT: F 357 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6903 (p0) REVERT: F 367 TYR cc_start: 0.7446 (t80) cc_final: 0.7116 (t80) REVERT: F 415 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: F 490 GLN cc_start: 0.7405 (tp40) cc_final: 0.7178 (mm-40) REVERT: F 738 GLU cc_start: 0.7846 (mp0) cc_final: 0.7614 (mp0) REVERT: F 943 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7923 (mtpp) REVERT: F 963 GLU cc_start: 0.6832 (mp0) cc_final: 0.6499 (mp0) REVERT: F 1338 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: G 40 LYS cc_start: 0.8313 (mttt) cc_final: 0.8059 (ttmt) REVERT: G 42 GLU cc_start: 0.5993 (pm20) cc_final: 0.5665 (tm-30) REVERT: G 87 LYS cc_start: 0.6782 (tttp) cc_final: 0.6208 (tptt) REVERT: G 192 MET cc_start: 0.8395 (ptm) cc_final: 0.8171 (ptm) REVERT: G 204 GLU cc_start: 0.6518 (tt0) cc_final: 0.5858 (mt-10) REVERT: G 213 LYS cc_start: 0.6715 (ptpt) cc_final: 0.6506 (pttt) REVERT: G 290 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6919 (tp) REVERT: G 322 ARG cc_start: 0.6522 (tpp-160) cc_final: 0.6064 (ptp90) REVERT: G 370 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8665 (ptpp) REVERT: G 371 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8026 (mtmm) REVERT: G 712 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7717 (mt0) REVERT: G 747 MET cc_start: 0.9037 (mmp) cc_final: 0.8774 (mmp) REVERT: G 833 GLU cc_start: 0.7917 (tp30) cc_final: 0.7503 (tp30) REVERT: G 1205 GLU cc_start: 0.7582 (tt0) cc_final: 0.7228 (tt0) REVERT: G 1215 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: G 1327 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: H 62 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7210 (tm-30) outliers start: 43 outliers final: 12 residues processed: 318 average time/residue: 1.7883 time to fit residues: 645.5915 Evaluate side-chains 292 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 357 ASN Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 618 GLN Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1338 GLU Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 712 GLN Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1095 MET Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1215 GLU Chi-restraints excluded: chain G residue 1327 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 178 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 GLN F1023 HIS G 708 ASN ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1019 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.145237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.091568 restraints weight = 43310.923| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.89 r_work: 0.2962 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 26339 Z= 0.243 Angle : 0.623 10.626 35798 Z= 0.329 Chirality : 0.046 0.176 4090 Planarity : 0.005 0.087 4511 Dihedral : 11.678 73.837 4062 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.61 % Rotamer: Outliers : 2.08 % Allowed : 11.16 % Favored : 86.76 % 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: 0.54 (0.15), residues: 3150 helix: 1.02 (0.15), residues: 1144 sheet: 0.09 (0.24), residues: 386 loop : 0.05 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G1193 HIS 0.007 0.001 HIS F1237 PHE 0.017 0.002 PHE G 116 TYR 0.019 0.002 TYR G 140 ARG 0.011 0.001 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 1138) hydrogen bonds : angle 5.05859 ( 3117) metal coordination : bond 0.00792 ( 8) metal coordination : angle 4.53321 ( 12) covalent geometry : bond 0.00572 (26331) covalent geometry : angle 0.61791 (35786) *********************** 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 to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7963 (mp10) REVERT: E 58 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7770 (mt-10) REVERT: E 99 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8530 (mm) REVERT: E 193 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: F 284 LEU cc_start: 0.5730 (mm) cc_final: 0.5303 (mm) REVERT: F 299 LYS cc_start: 0.6406 (ttpt) cc_final: 0.6190 (ttpt) REVERT: F 337 PHE cc_start: 0.6627 (t80) cc_final: 0.6377 (t80) REVERT: F 357 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.6938 (p0) REVERT: F 367 TYR cc_start: 0.7431 (t80) cc_final: 0.7124 (t80) REVERT: F 415 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: F 490 GLN cc_start: 0.7480 (tp40) cc_final: 0.7226 (mm-40) REVERT: F 943 LYS cc_start: 0.8284 (mtmt) cc_final: 0.8009 (mtpp) REVERT: F 1338 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: G 40 LYS cc_start: 0.8339 (mttt) cc_final: 0.8079 (ttmt) REVERT: G 42 GLU cc_start: 0.6135 (pm20) cc_final: 0.5721 (tm-30) REVERT: G 87 LYS cc_start: 0.6884 (tttp) cc_final: 0.6291 (tptt) REVERT: G 192 MET cc_start: 0.8416 (ptm) cc_final: 0.8144 (ptm) REVERT: G 204 GLU cc_start: 0.6477 (tt0) cc_final: 0.5798 (mt-10) REVERT: G 290 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6880 (tp) REVERT: G 370 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8657 (ptpp) REVERT: G 371 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8132 (mtmm) REVERT: G 802 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8392 (t0) REVERT: G 1205 GLU cc_start: 0.7507 (tt0) cc_final: 0.7180 (tt0) REVERT: G 1215 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: G 1327 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8679 (mt-10) outliers start: 56 outliers final: 29 residues processed: 311 average time/residue: 1.7402 time to fit residues: 609.8630 Evaluate side-chains 306 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 357 ASN Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 441 GLU Chi-restraints excluded: chain F residue 618 GLN Chi-restraints excluded: chain F residue 634 VAL Chi-restraints excluded: chain F residue 1041 ASP Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1338 GLU Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 705 THR Chi-restraints excluded: chain G residue 709 ARG Chi-restraints excluded: chain G residue 802 ASP Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 931 THR Chi-restraints excluded: chain G residue 953 LYS Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1095 MET Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1175 LEU Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1215 GLU Chi-restraints excluded: chain G residue 1243 LEU Chi-restraints excluded: chain G residue 1327 GLU Chi-restraints excluded: chain G residue 1371 ARG Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 211 optimal weight: 0.9990 chunk 104 optimal weight: 0.0050 chunk 124 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 109 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 216 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 GLN F 628 HIS G 708 ASN G 875 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.149357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095187 restraints weight = 61975.840| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.24 r_work: 0.3012 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26339 Z= 0.108 Angle : 0.516 8.673 35798 Z= 0.271 Chirality : 0.041 0.145 4090 Planarity : 0.004 0.059 4511 Dihedral : 11.436 73.560 4062 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 1.41 % Allowed : 12.50 % Favored : 86.10 % 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: 0.79 (0.15), residues: 3150 helix: 1.36 (0.15), residues: 1135 sheet: 0.14 (0.24), residues: 392 loop : 0.13 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G1193 HIS 0.005 0.001 HIS G 104 PHE 0.015 0.001 PHE F 812 TYR 0.015 0.001 TYR G 140 ARG 0.016 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 1138) hydrogen bonds : angle 4.72709 ( 3117) metal coordination : bond 0.00511 ( 8) metal coordination : angle 3.55540 ( 12) covalent geometry : bond 0.00237 (26331) covalent geometry : angle 0.51162 (35786) *********************** 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 332 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 29 GLU cc_start: 0.8667 (tt0) cc_final: 0.8346 (tt0) REVERT: E 58 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7692 (mt-10) REVERT: E 193 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6072 (mp0) REVERT: F 218 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7477 (pp20) REVERT: F 284 LEU cc_start: 0.5628 (mm) cc_final: 0.5204 (mm) REVERT: F 299 LYS cc_start: 0.6267 (ttpt) cc_final: 0.5947 (ttpt) REVERT: F 337 PHE cc_start: 0.6287 (t80) cc_final: 0.6039 (t80) REVERT: F 367 TYR cc_start: 0.7357 (t80) cc_final: 0.7100 (t80) REVERT: F 490 GLN cc_start: 0.7318 (tp40) cc_final: 0.7100 (mm-40) REVERT: F 943 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7945 (mtpp) REVERT: F 1338 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: G 40 LYS cc_start: 0.8354 (mttt) cc_final: 0.8107 (ttmt) REVERT: G 42 GLU cc_start: 0.6031 (pm20) cc_final: 0.5579 (tm-30) REVERT: G 78 LEU cc_start: 0.7163 (tm) cc_final: 0.6494 (pp) REVERT: G 87 LYS cc_start: 0.6888 (tttp) cc_final: 0.6284 (tptt) REVERT: G 171 GLU cc_start: 0.6441 (tt0) cc_final: 0.6206 (pt0) REVERT: G 192 MET cc_start: 0.8368 (ptm) cc_final: 0.8086 (ptm) REVERT: G 204 GLU cc_start: 0.6517 (tt0) cc_final: 0.5864 (mt-10) REVERT: G 290 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6782 (tp) REVERT: G 370 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8649 (ptpp) REVERT: G 371 LYS cc_start: 0.8435 (mtmm) cc_final: 0.7986 (mtmm) REVERT: G 562 GLU cc_start: 0.7520 (mp0) cc_final: 0.7285 (pm20) REVERT: G 1205 GLU cc_start: 0.7455 (tt0) cc_final: 0.7141 (tt0) REVERT: G 1327 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8623 (mt-10) REVERT: H 62 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7193 (tm-30) outliers start: 38 outliers final: 13 residues processed: 317 average time/residue: 1.8238 time to fit residues: 651.9537 Evaluate side-chains 288 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 269 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 441 GLU Chi-restraints excluded: chain F residue 1338 GLU Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1095 MET Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1175 LEU Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1243 LEU Chi-restraints excluded: chain G residue 1327 GLU Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 207 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 189 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 GLN F1220 GLN G 708 ASN G1019 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.092795 restraints weight = 55926.474| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.35 r_work: 0.2958 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26339 Z= 0.187 Angle : 0.571 9.128 35798 Z= 0.301 Chirality : 0.044 0.161 4090 Planarity : 0.005 0.076 4511 Dihedral : 11.530 73.771 4062 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 1.82 % Allowed : 12.57 % Favored : 85.61 % 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: 0.68 (0.15), residues: 3150 helix: 1.22 (0.15), residues: 1143 sheet: 0.07 (0.24), residues: 392 loop : 0.10 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G1193 HIS 0.006 0.001 HIS F1237 PHE 0.015 0.002 PHE G1319 TYR 0.016 0.002 TYR G 631 ARG 0.017 0.001 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 1138) hydrogen bonds : angle 4.86551 ( 3117) metal coordination : bond 0.00631 ( 8) metal coordination : angle 3.74443 ( 12) covalent geometry : bond 0.00437 (26331) covalent geometry : angle 0.56672 (35786) *********************** 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 316 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 267 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7704 (mt-10) REVERT: E 193 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6204 (mp0) REVERT: E 205 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8272 (ttt) REVERT: F 284 LEU cc_start: 0.5646 (mm) cc_final: 0.5229 (mm) REVERT: F 299 LYS cc_start: 0.6218 (ttpt) cc_final: 0.5988 (ttpt) REVERT: F 337 PHE cc_start: 0.6468 (t80) cc_final: 0.6177 (t80) REVERT: F 367 TYR cc_start: 0.7320 (t80) cc_final: 0.7079 (t80) REVERT: F 415 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: F 490 GLN cc_start: 0.7401 (tp40) cc_final: 0.7149 (mm-40) REVERT: F 943 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7996 (mtpp) REVERT: F 1033 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7217 (ttp-170) REVERT: F 1338 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: G 40 LYS cc_start: 0.8342 (mttt) cc_final: 0.8140 (ttmt) REVERT: G 42 GLU cc_start: 0.6083 (pm20) cc_final: 0.5625 (tm-30) REVERT: G 78 LEU cc_start: 0.7171 (tm) cc_final: 0.6494 (pp) REVERT: G 87 LYS cc_start: 0.6898 (tttp) cc_final: 0.6283 (tptt) REVERT: G 192 MET cc_start: 0.8377 (ptm) cc_final: 0.8098 (ptm) REVERT: G 197 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: G 204 GLU cc_start: 0.6526 (tt0) cc_final: 0.5870 (mt-10) REVERT: G 216 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6627 (tptt) REVERT: G 290 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6750 (tp) REVERT: G 370 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8712 (ptpp) REVERT: G 371 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8036 (mtmm) REVERT: G 1205 GLU cc_start: 0.7420 (tt0) cc_final: 0.7108 (tt0) REVERT: G 1327 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: G 1370 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7180 (mtm) outliers start: 49 outliers final: 21 residues processed: 301 average time/residue: 1.7902 time to fit residues: 606.1578 Evaluate side-chains 294 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 441 GLU Chi-restraints excluded: chain F residue 1033 ARG Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1338 GLU Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1095 MET Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1175 LEU Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1243 LEU Chi-restraints excluded: chain G residue 1327 GLU Chi-restraints excluded: chain G residue 1370 MET Chi-restraints excluded: chain G residue 1371 ARG Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 183 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 68 optimal weight: 0.0470 chunk 163 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 HIS F 618 GLN F 628 HIS F1220 GLN G1019 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091429 restraints weight = 48950.912| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.01 r_work: 0.2963 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 26339 Z= 0.214 Angle : 0.598 9.590 35798 Z= 0.316 Chirality : 0.045 0.205 4090 Planarity : 0.005 0.102 4511 Dihedral : 11.605 73.824 4062 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 2.11 % Allowed : 12.98 % Favored : 84.91 % 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: 0.60 (0.15), residues: 3150 helix: 1.16 (0.15), residues: 1135 sheet: -0.00 (0.24), residues: 397 loop : 0.07 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G1193 HIS 0.007 0.001 HIS F1023 PHE 0.015 0.002 PHE G 116 TYR 0.017 0.002 TYR G 140 ARG 0.018 0.001 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 1138) hydrogen bonds : angle 4.94967 ( 3117) metal coordination : bond 0.00691 ( 8) metal coordination : angle 3.94850 ( 12) covalent geometry : bond 0.00501 (26331) covalent geometry : angle 0.59390 (35786) *********************** 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 332 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 18 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7933 (mp10) REVERT: E 58 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7745 (mt-10) REVERT: E 193 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: E 205 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8217 (ttt) REVERT: F 284 LEU cc_start: 0.5678 (mm) cc_final: 0.5238 (mm) REVERT: F 299 LYS cc_start: 0.6386 (ttpt) cc_final: 0.6137 (ttpt) REVERT: F 337 PHE cc_start: 0.6615 (t80) cc_final: 0.6340 (t80) REVERT: F 357 ASN cc_start: 0.7330 (OUTLIER) cc_final: 0.6981 (p0) REVERT: F 367 TYR cc_start: 0.7418 (t80) cc_final: 0.7156 (t80) REVERT: F 415 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: F 490 GLN cc_start: 0.7444 (tp40) cc_final: 0.7181 (mm-40) REVERT: F 943 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7991 (mtpp) REVERT: F 1338 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: G 40 LYS cc_start: 0.8402 (mttt) cc_final: 0.8058 (ttmt) REVERT: G 78 LEU cc_start: 0.7147 (tm) cc_final: 0.6534 (pp) REVERT: G 87 LYS cc_start: 0.7005 (tttp) cc_final: 0.6355 (tptt) REVERT: G 192 MET cc_start: 0.8324 (ptm) cc_final: 0.8107 (ptm) REVERT: G 204 GLU cc_start: 0.6514 (tt0) cc_final: 0.5846 (mt-10) REVERT: G 216 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6631 (tptt) REVERT: G 290 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6854 (tp) REVERT: G 370 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8649 (ptpp) REVERT: G 371 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8094 (mtmm) REVERT: G 562 GLU cc_start: 0.7423 (mp0) cc_final: 0.7113 (pm20) REVERT: G 1189 MET cc_start: 0.7231 (mpp) cc_final: 0.7020 (mmp) REVERT: G 1205 GLU cc_start: 0.7431 (tt0) cc_final: 0.7159 (tt0) REVERT: G 1215 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: G 1298 VAL cc_start: 0.6884 (p) cc_final: 0.6553 (t) REVERT: G 1327 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8677 (mt-10) REVERT: G 1370 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7184 (mtm) outliers start: 57 outliers final: 26 residues processed: 311 average time/residue: 1.7241 time to fit residues: 607.4755 Evaluate side-chains 307 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 357 ASN Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 862 LEU Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1338 GLU Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 705 THR Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 931 THR Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1175 LEU Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1215 GLU Chi-restraints excluded: chain G residue 1243 LEU Chi-restraints excluded: chain G residue 1327 GLU Chi-restraints excluded: chain G residue 1370 MET Chi-restraints excluded: chain G residue 1371 ARG Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 194 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 263 optimal weight: 0.0970 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 GLN F 628 HIS G 708 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.149009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095650 restraints weight = 51899.748| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.06 r_work: 0.3022 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26339 Z= 0.117 Angle : 0.518 8.857 35798 Z= 0.273 Chirality : 0.042 0.163 4090 Planarity : 0.004 0.071 4511 Dihedral : 11.374 73.585 4062 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Rotamer: Outliers : 1.33 % Allowed : 14.28 % Favored : 84.39 % 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: 0.78 (0.15), residues: 3150 helix: 1.36 (0.15), residues: 1143 sheet: 0.19 (0.25), residues: 390 loop : 0.10 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1193 HIS 0.004 0.001 HIS G 104 PHE 0.014 0.001 PHE G1319 TYR 0.014 0.001 TYR G 631 ARG 0.019 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 1138) hydrogen bonds : angle 4.65879 ( 3117) metal coordination : bond 0.00470 ( 8) metal coordination : angle 3.19163 ( 12) covalent geometry : bond 0.00263 (26331) covalent geometry : angle 0.51443 (35786) *********************** 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 318 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.8075 (mmt-90) REVERT: E 29 GLU cc_start: 0.8717 (tt0) cc_final: 0.8373 (tt0) REVERT: E 58 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7642 (mt-10) REVERT: E 93 GLN cc_start: 0.7296 (mp10) cc_final: 0.6981 (mp10) REVERT: E 193 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: F 284 LEU cc_start: 0.5643 (mm) cc_final: 0.5199 (mm) REVERT: F 299 LYS cc_start: 0.6249 (ttpt) cc_final: 0.6005 (ttpt) REVERT: F 337 PHE cc_start: 0.6300 (t80) cc_final: 0.6033 (t80) REVERT: F 415 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: F 490 GLN cc_start: 0.7315 (tp40) cc_final: 0.7092 (mm-40) REVERT: F 943 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7977 (mtpp) REVERT: F 1338 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: G 40 LYS cc_start: 0.8404 (mttt) cc_final: 0.8204 (ttmt) REVERT: G 42 GLU cc_start: 0.6105 (pm20) cc_final: 0.5615 (tm-30) REVERT: G 78 LEU cc_start: 0.7158 (tm) cc_final: 0.6459 (pp) REVERT: G 87 LYS cc_start: 0.6987 (tttp) cc_final: 0.6291 (tptt) REVERT: G 155 GLU cc_start: 0.6318 (pm20) cc_final: 0.5923 (tm-30) REVERT: G 192 MET cc_start: 0.8303 (ptm) cc_final: 0.8024 (ptm) REVERT: G 204 GLU cc_start: 0.6634 (tt0) cc_final: 0.5997 (mt-10) REVERT: G 216 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6659 (tptt) REVERT: G 290 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6721 (tp) REVERT: G 370 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8657 (ptpp) REVERT: G 371 LYS cc_start: 0.8360 (mtmm) cc_final: 0.7914 (mtmm) REVERT: G 562 GLU cc_start: 0.7330 (mp0) cc_final: 0.7081 (pm20) REVERT: G 1200 GLU cc_start: 0.5812 (mp0) cc_final: 0.4605 (tp30) REVERT: G 1205 GLU cc_start: 0.7460 (tt0) cc_final: 0.7140 (tt0) REVERT: G 1215 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: G 1327 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: H 62 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7191 (tm-30) outliers start: 35 outliers final: 14 residues processed: 304 average time/residue: 1.8023 time to fit residues: 615.5908 Evaluate side-chains 289 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 862 LEU Chi-restraints excluded: chain F residue 1338 GLU Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1175 LEU Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1215 GLU Chi-restraints excluded: chain G residue 1243 LEU Chi-restraints excluded: chain G residue 1327 GLU Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 74 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 GLN F1220 GLN G 708 ASN G 817 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.146223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091761 restraints weight = 54951.482| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.12 r_work: 0.2964 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26339 Z= 0.198 Angle : 0.583 9.206 35798 Z= 0.308 Chirality : 0.044 0.241 4090 Planarity : 0.005 0.080 4511 Dihedral : 11.521 73.787 4062 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 1.59 % Allowed : 14.28 % Favored : 84.13 % 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: 0.66 (0.15), residues: 3150 helix: 1.22 (0.15), residues: 1143 sheet: -0.01 (0.24), residues: 407 loop : 0.10 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1193 HIS 0.006 0.001 HIS F1023 PHE 0.015 0.002 PHE G1319 TYR 0.016 0.002 TYR G 631 ARG 0.019 0.001 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 1138) hydrogen bonds : angle 4.84893 ( 3117) metal coordination : bond 0.00606 ( 8) metal coordination : angle 3.61744 ( 12) covalent geometry : bond 0.00464 (26331) covalent geometry : angle 0.57967 (35786) *********************** 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 309 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7782 (mt-10) REVERT: E 193 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: F 284 LEU cc_start: 0.5696 (mm) cc_final: 0.5239 (mm) REVERT: F 299 LYS cc_start: 0.6352 (ttpt) cc_final: 0.6103 (ttpt) REVERT: F 337 PHE cc_start: 0.6563 (t80) cc_final: 0.6269 (t80) REVERT: F 415 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: F 490 GLN cc_start: 0.7428 (tp40) cc_final: 0.7175 (mm-40) REVERT: F 943 LYS cc_start: 0.8263 (mtmt) cc_final: 0.8022 (mtpp) REVERT: F 1085 MET cc_start: 0.9325 (mmm) cc_final: 0.9081 (mmm) REVERT: F 1338 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: G 40 LYS cc_start: 0.8425 (mttt) cc_final: 0.8084 (ttmt) REVERT: G 78 LEU cc_start: 0.7167 (tm) cc_final: 0.6462 (pp) REVERT: G 87 LYS cc_start: 0.7013 (tttp) cc_final: 0.6354 (tptt) REVERT: G 155 GLU cc_start: 0.6264 (pm20) cc_final: 0.5903 (tm-30) REVERT: G 192 MET cc_start: 0.8335 (ptm) cc_final: 0.8057 (ptm) REVERT: G 204 GLU cc_start: 0.6626 (tt0) cc_final: 0.5984 (mt-10) REVERT: G 216 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6617 (tptt) REVERT: G 290 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6853 (tp) REVERT: G 370 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8689 (ptpp) REVERT: G 371 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8010 (mtmm) REVERT: G 562 GLU cc_start: 0.7338 (mp0) cc_final: 0.7064 (pm20) REVERT: G 802 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8340 (t70) REVERT: G 860 ARG cc_start: 0.6775 (tpt-90) cc_final: 0.6556 (tpt-90) REVERT: G 1200 GLU cc_start: 0.5952 (mp0) cc_final: 0.4599 (tp30) REVERT: G 1205 GLU cc_start: 0.7448 (tt0) cc_final: 0.7130 (tt0) REVERT: G 1215 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: G 1298 VAL cc_start: 0.6851 (p) cc_final: 0.6508 (t) REVERT: G 1327 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8689 (mt-10) outliers start: 42 outliers final: 21 residues processed: 299 average time/residue: 1.7526 time to fit residues: 594.8771 Evaluate side-chains 294 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 441 GLU Chi-restraints excluded: chain F residue 634 VAL Chi-restraints excluded: chain F residue 862 LEU Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1338 GLU Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 705 THR Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 802 ASP Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 994 SER Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1175 LEU Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1215 GLU Chi-restraints excluded: chain G residue 1243 LEU Chi-restraints excluded: chain G residue 1327 GLU Chi-restraints excluded: chain G residue 1371 ARG Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 208 optimal weight: 0.6980 chunk 224 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 84 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 GLN F 628 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.148174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.094410 restraints weight = 62140.942| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.40 r_work: 0.2988 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26339 Z= 0.129 Angle : 0.533 9.135 35798 Z= 0.281 Chirality : 0.042 0.212 4090 Planarity : 0.005 0.072 4511 Dihedral : 11.401 73.636 4062 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 1.26 % Allowed : 14.57 % Favored : 84.17 % 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: 0.77 (0.15), residues: 3150 helix: 1.34 (0.15), residues: 1144 sheet: 0.14 (0.25), residues: 390 loop : 0.11 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G1193 HIS 0.004 0.001 HIS F1237 PHE 0.015 0.001 PHE G1319 TYR 0.014 0.001 TYR G 631 ARG 0.019 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 1138) hydrogen bonds : angle 4.69050 ( 3117) metal coordination : bond 0.00504 ( 8) metal coordination : angle 3.20092 ( 12) covalent geometry : bond 0.00295 (26331) covalent geometry : angle 0.52977 (35786) ********************** 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 305 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 ARG cc_start: 0.8293 (mmt-90) cc_final: 0.8040 (mmt-90) REVERT: E 18 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: E 58 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7716 (mt-10) REVERT: E 93 GLN cc_start: 0.7271 (mp10) cc_final: 0.6946 (mp10) REVERT: E 193 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5983 (mp0) REVERT: F 284 LEU cc_start: 0.5475 (mm) cc_final: 0.5036 (mm) REVERT: F 299 LYS cc_start: 0.6199 (ttpt) cc_final: 0.5959 (ttpt) REVERT: F 337 PHE cc_start: 0.6393 (t80) cc_final: 0.6092 (t80) REVERT: F 415 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: F 490 GLN cc_start: 0.7313 (tp40) cc_final: 0.7071 (mm-40) REVERT: F 943 LYS cc_start: 0.8245 (mtmt) cc_final: 0.8001 (mtpp) REVERT: F 1338 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: G 40 LYS cc_start: 0.8416 (mttt) cc_final: 0.8097 (ttmt) REVERT: G 78 LEU cc_start: 0.7138 (tm) cc_final: 0.6490 (pp) REVERT: G 87 LYS cc_start: 0.6989 (tttp) cc_final: 0.6301 (tptt) REVERT: G 155 GLU cc_start: 0.6322 (pm20) cc_final: 0.5958 (tm-30) REVERT: G 192 MET cc_start: 0.8301 (ptm) cc_final: 0.8048 (ptm) REVERT: G 204 GLU cc_start: 0.6642 (tt0) cc_final: 0.6007 (mt-10) REVERT: G 216 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6550 (tptt) REVERT: G 290 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6751 (tp) REVERT: G 370 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8665 (ptpp) REVERT: G 371 LYS cc_start: 0.8381 (mtmm) cc_final: 0.7914 (mtmm) REVERT: G 562 GLU cc_start: 0.7278 (mp0) cc_final: 0.7042 (pm20) REVERT: G 1200 GLU cc_start: 0.5881 (mp0) cc_final: 0.4509 (tp30) REVERT: G 1205 GLU cc_start: 0.7461 (tt0) cc_final: 0.7158 (tt0) REVERT: G 1215 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: G 1327 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8686 (mt-10) REVERT: H 62 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7239 (tm-30) outliers start: 33 outliers final: 18 residues processed: 294 average time/residue: 1.7178 time to fit residues: 570.0655 Evaluate side-chains 295 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 417 SER Chi-restraints excluded: chain F residue 862 LEU Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1338 GLU Chi-restraints excluded: chain G residue 70 CYS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain G residue 430 HIS Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1163 VAL Chi-restraints excluded: chain G residue 1175 LEU Chi-restraints excluded: chain G residue 1178 THR Chi-restraints excluded: chain G residue 1215 GLU Chi-restraints excluded: chain G residue 1243 LEU Chi-restraints excluded: chain G residue 1327 GLU Chi-restraints excluded: chain G residue 1371 ARG Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 19 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 76 optimal weight: 0.4980 chunk 177 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 312 optimal weight: 5.9990 chunk 129 optimal weight: 0.0770 chunk 214 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN F 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.148832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095258 restraints weight = 62712.639| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.42 r_work: 0.3016 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26339 Z= 0.111 Angle : 0.513 9.127 35798 Z= 0.270 Chirality : 0.041 0.186 4090 Planarity : 0.004 0.078 4511 Dihedral : 11.304 73.610 4062 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.80 % Rotamer: Outliers : 1.11 % Allowed : 14.83 % Favored : 84.06 % 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: 0.86 (0.15), residues: 3150 helix: 1.41 (0.15), residues: 1150 sheet: 0.20 (0.25), residues: 380 loop : 0.15 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1193 HIS 0.004 0.001 HIS G 104 PHE 0.015 0.001 PHE G1319 TYR 0.013 0.001 TYR G 631 ARG 0.019 0.000 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1138) hydrogen bonds : angle 4.56124 ( 3117) metal coordination : bond 0.00429 ( 8) metal coordination : angle 2.84348 ( 12) covalent geometry : bond 0.00251 (26331) covalent geometry : angle 0.51013 (35786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29419.56 seconds wall clock time: 506 minutes 31.54 seconds (30391.54 seconds total)