Starting phenix.real_space_refine on Mon Aug 25 08:05:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fvr_29491/08_2025/8fvr_29491.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fvr_29491/08_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_29491/08_2025/8fvr_29491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fvr_29491/08_2025/8fvr_29491.map" model { file = "/net/cci-nas-00/data/ceres_data/8fvr_29491/08_2025/8fvr_29491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fvr_29491/08_2025/8fvr_29491.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 1, 'GLN:plan1': 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: 9.25, per 1000 atoms: 0.36 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: 2.49 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.90 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: 7.70 Time building geometry restraints manager: 3.31 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 38.390 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG G1148 TYR 0.015 0.001 TYR G1186 PHE 0.013 0.002 PHE F1164 TRP 0.018 0.002 TRP G1193 HIS 0.005 0.001 HIS F1070 Details of bonding type rmsd covalent geometry : bond 0.00342 (26331) covalent geometry : angle 0.64262 (35786) hydrogen bonds : bond 0.14232 ( 1138) hydrogen bonds : angle 6.27896 ( 3117) metal coordination : bond 0.02706 ( 8) metal coordination : angle 18.59381 ( 12) *********************** 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 : 1.084 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: 0.9595 time to fit residues: 450.1333 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 : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN 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 G 708 ASN G1019 ASN H 15 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.146547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091786 restraints weight = 52609.354| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.04 r_work: 0.2965 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- 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 = 0.35 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: 0.8702 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26339 Z= 0.236 Angle : 0.660 10.723 35798 Z= 0.348 Chirality : 0.047 0.184 4090 Planarity : 0.005 0.082 4511 Dihedral : 11.635 73.805 4062 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.97 % Allowed : 8.08 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.15), residues: 3150 helix: 1.09 (0.15), residues: 1141 sheet: 0.25 (0.25), residues: 385 loop : 0.02 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 143 TYR 0.022 0.002 TYR G 140 PHE 0.020 0.002 PHE F 337 TRP 0.014 0.002 TRP F 997 HIS 0.008 0.002 HIS G 777 Details of bonding type rmsd covalent geometry : bond 0.00555 (26331) covalent geometry : angle 0.65192 (35786) hydrogen bonds : bond 0.05227 ( 1138) hydrogen bonds : angle 5.21296 ( 3117) metal coordination : bond 0.01034 ( 8) metal coordination : angle 5.48871 ( 12) *********************** 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 351 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7706 (mt-10) REVERT: E 125 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7989 (ptmm) REVERT: F 299 LYS cc_start: 0.6445 (ttpt) cc_final: 0.6175 (ttpt) REVERT: F 339 ASN cc_start: 0.7336 (m-40) cc_final: 0.7088 (m-40) REVERT: F 376 PRO cc_start: 0.7734 (Cg_endo) cc_final: 0.7318 (Cg_exo) REVERT: F 415 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: F 490 GLN cc_start: 0.7439 (tp40) cc_final: 0.7179 (mm-40) REVERT: F 738 GLU cc_start: 0.7997 (mp0) cc_final: 0.7668 (mp0) REVERT: F 943 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7946 (mtpp) REVERT: F 963 GLU cc_start: 0.6837 (mp0) cc_final: 0.6379 (mp0) REVERT: G 40 LYS cc_start: 0.8307 (mttt) cc_final: 0.8053 (ttmt) REVERT: G 42 GLU cc_start: 0.5867 (pm20) cc_final: 0.5629 (tm-30) REVERT: G 87 LYS cc_start: 0.6708 (tttp) cc_final: 0.6184 (tptt) REVERT: G 134 ASP cc_start: 0.7922 (m-30) cc_final: 0.7708 (m-30) REVERT: G 158 GLN cc_start: 0.7448 (tt0) cc_final: 0.7199 (tt0) REVERT: G 196 GLN cc_start: 0.7706 (tt0) cc_final: 0.7311 (tm-30) REVERT: G 204 GLU cc_start: 0.6516 (tt0) cc_final: 0.5831 (mt-10) REVERT: G 290 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6952 (tp) REVERT: G 320 ASN cc_start: 0.7068 (t0) cc_final: 0.6810 (t0) REVERT: G 371 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8089 (mtmm) REVERT: G 1205 GLU cc_start: 0.7570 (tt0) cc_final: 0.7296 (tt0) REVERT: G 1327 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8577 (mt-10) REVERT: H 62 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7249 (tm-30) outliers start: 53 outliers final: 18 residues processed: 326 average time/residue: 0.9534 time to fit residues: 348.6585 Evaluate side-chains 296 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 274 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 1041 ASP 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 290 ILE Chi-restraints excluded: chain G residue 674 THR Chi-restraints excluded: chain G residue 705 THR Chi-restraints excluded: chain G residue 712 GLN Chi-restraints excluded: chain G residue 812 ASP Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 931 THR Chi-restraints excluded: chain G residue 985 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 315 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN F 618 GLN F 628 HIS F1023 HIS G 80 HIS G 186 GLN G 708 ASN ** G 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 968 ASN G1019 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.146213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.091870 restraints weight = 53131.335| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.07 r_work: 0.2963 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 26339 Z= 0.209 Angle : 0.604 9.853 35798 Z= 0.319 Chirality : 0.046 0.173 4090 Planarity : 0.005 0.069 4511 Dihedral : 11.638 73.737 4062 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.30 % Allowed : 9.08 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.15), residues: 3150 helix: 1.10 (0.15), residues: 1139 sheet: 0.16 (0.24), residues: 387 loop : 0.05 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 143 TYR 0.023 0.002 TYR G 140 PHE 0.018 0.002 PHE F 812 TRP 0.014 0.002 TRP G1193 HIS 0.007 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00487 (26331) covalent geometry : angle 0.59811 (35786) hydrogen bonds : bond 0.04817 ( 1138) hydrogen bonds : angle 5.04202 ( 3117) metal coordination : bond 0.00820 ( 8) metal coordination : angle 4.49015 ( 12) *********************** 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 343 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 281 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: E 58 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7736 (mt-10) REVERT: E 99 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8485 (mm) REVERT: E 193 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: F 103 VAL cc_start: 0.6844 (t) cc_final: 0.6617 (m) REVERT: F 239 MET cc_start: 0.3773 (tmm) cc_final: 0.3554 (tmm) REVERT: F 284 LEU cc_start: 0.5962 (mm) cc_final: 0.5581 (mm) REVERT: F 337 PHE cc_start: 0.6905 (t80) cc_final: 0.6658 (t80) REVERT: F 357 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6899 (p0) REVERT: F 367 TYR cc_start: 0.7418 (t80) cc_final: 0.7168 (t80) REVERT: F 490 GLN cc_start: 0.7449 (tp40) cc_final: 0.7209 (mm-40) REVERT: F 738 GLU cc_start: 0.7969 (mp0) cc_final: 0.7722 (mp0) REVERT: F 943 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7999 (mtpp) REVERT: F 1085 MET cc_start: 0.9324 (mmm) cc_final: 0.9083 (mmm) REVERT: F 1338 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: G 40 LYS cc_start: 0.8332 (mttt) cc_final: 0.8071 (ttmt) REVERT: G 42 GLU cc_start: 0.6129 (pm20) cc_final: 0.5725 (tm-30) REVERT: G 87 LYS cc_start: 0.6859 (tttp) cc_final: 0.6270 (tptt) REVERT: G 158 GLN cc_start: 0.7395 (tt0) cc_final: 0.7148 (tt0) REVERT: G 192 MET cc_start: 0.8420 (ptm) cc_final: 0.8181 (ptm) REVERT: G 204 GLU cc_start: 0.6495 (tt0) cc_final: 0.5830 (mt-10) REVERT: G 290 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6831 (tp) REVERT: G 371 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8100 (mtmm) REVERT: G 712 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7731 (mt0) REVERT: G 833 GLU cc_start: 0.8007 (tp30) cc_final: 0.7611 (tp30) REVERT: G 860 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6210 (ttt90) REVERT: G 1205 GLU cc_start: 0.7535 (tt0) cc_final: 0.7204 (tt0) REVERT: G 1215 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: G 1291 GLU cc_start: 0.7144 (tp30) cc_final: 0.6927 (tp30) REVERT: G 1327 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8564 (mt-10) outliers start: 62 outliers final: 23 residues processed: 317 average time/residue: 0.9290 time to fit residues: 331.1840 Evaluate side-chains 296 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 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 386 GLU Chi-restraints excluded: chain G residue 499 ILE 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 860 ARG Chi-restraints excluded: chain G residue 931 THR 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 1327 GLU Chi-restraints excluded: chain G residue 1371 ARG Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 168 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 232 optimal weight: 0.0000 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 286 optimal weight: 0.0870 overall best weight: 0.7164 ------------------------------------------------------------------------------- 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 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095469 restraints weight = 54299.362| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.12 r_work: 0.3021 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26339 Z= 0.114 Angle : 0.520 8.038 35798 Z= 0.274 Chirality : 0.042 0.144 4090 Planarity : 0.004 0.056 4511 Dihedral : 11.423 73.569 4062 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.52 % Allowed : 10.90 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3150 helix: 1.39 (0.16), residues: 1134 sheet: 0.26 (0.24), residues: 400 loop : 0.15 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 143 TYR 0.017 0.001 TYR G 140 PHE 0.018 0.001 PHE F 812 TRP 0.018 0.001 TRP G1193 HIS 0.005 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00252 (26331) covalent geometry : angle 0.51618 (35786) hydrogen bonds : bond 0.03719 ( 1138) hydrogen bonds : angle 4.73521 ( 3117) metal coordination : bond 0.00525 ( 8) metal coordination : angle 3.66738 ( 12) *********************** 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 337 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 296 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7895 (mmp80) REVERT: E 58 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7608 (mt-10) REVERT: E 67 GLU cc_start: 0.7004 (tp30) cc_final: 0.6711 (tp30) REVERT: F 103 VAL cc_start: 0.6846 (t) cc_final: 0.6603 (m) REVERT: F 239 MET cc_start: 0.3577 (tmm) cc_final: 0.3332 (tmm) REVERT: F 284 LEU cc_start: 0.5931 (mm) cc_final: 0.5594 (mm) REVERT: F 337 PHE cc_start: 0.6677 (t80) cc_final: 0.6380 (t80) REVERT: F 367 TYR cc_start: 0.7409 (t80) cc_final: 0.7165 (t80) REVERT: F 490 GLN cc_start: 0.7357 (tp40) cc_final: 0.7146 (mm-40) REVERT: F 943 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7952 (mtpp) REVERT: F 1338 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: G 40 LYS cc_start: 0.8326 (mttt) cc_final: 0.8078 (ttmt) REVERT: G 42 GLU cc_start: 0.6036 (pm20) cc_final: 0.5546 (tm-30) REVERT: G 78 LEU cc_start: 0.7166 (tm) cc_final: 0.6541 (pp) REVERT: G 87 LYS cc_start: 0.6898 (tttp) cc_final: 0.6288 (tptt) REVERT: G 164 GLN cc_start: 0.6443 (OUTLIER) cc_final: 0.6222 (mt0) REVERT: G 192 MET cc_start: 0.8329 (ptm) cc_final: 0.8069 (ptm) REVERT: G 204 GLU cc_start: 0.6536 (tt0) cc_final: 0.5871 (mt-10) REVERT: G 278 ARG cc_start: 0.6787 (mtm110) cc_final: 0.6444 (mtm110) REVERT: G 290 ILE cc_start: 0.7122 (OUTLIER) cc_final: 0.6880 (tp) REVERT: G 370 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8646 (ptpp) REVERT: G 371 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7991 (mtmm) REVERT: G 1205 GLU cc_start: 0.7528 (tt0) cc_final: 0.7231 (tt0) REVERT: G 1215 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: G 1291 GLU cc_start: 0.7297 (tp30) cc_final: 0.7065 (tp30) REVERT: G 1327 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: H 62 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7241 (tm-30) outliers start: 41 outliers final: 11 residues processed: 319 average time/residue: 0.8664 time to fit residues: 310.3868 Evaluate side-chains 288 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain F residue 218 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 164 GLN 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 812 ASP Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1095 MET Chi-restraints excluded: chain G residue 1175 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 251 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 G 708 ASN G1019 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.146027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.091421 restraints weight = 62828.474| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.22 r_work: 0.2950 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 26339 Z= 0.212 Angle : 0.589 9.470 35798 Z= 0.311 Chirality : 0.045 0.159 4090 Planarity : 0.005 0.077 4511 Dihedral : 11.575 73.825 4062 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 1.89 % Allowed : 11.38 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.15), residues: 3150 helix: 1.21 (0.15), residues: 1141 sheet: 0.07 (0.24), residues: 395 loop : 0.12 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 143 TYR 0.018 0.002 TYR G 140 PHE 0.015 0.002 PHE G1319 TRP 0.018 0.002 TRP G1193 HIS 0.006 0.001 HIS F1023 Details of bonding type rmsd covalent geometry : bond 0.00498 (26331) covalent geometry : angle 0.58506 (35786) hydrogen bonds : bond 0.04693 ( 1138) hydrogen bonds : angle 4.92078 ( 3117) metal coordination : bond 0.00678 ( 8) metal coordination : angle 3.98717 ( 12) *********************** 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 314 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7802 (mt-10) REVERT: E 99 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8506 (mm) REVERT: E 193 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: E 205 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8551 (ttt) REVERT: F 103 VAL cc_start: 0.6821 (t) cc_final: 0.6616 (m) REVERT: F 239 MET cc_start: 0.3444 (tmm) cc_final: 0.3222 (tmm) REVERT: F 284 LEU cc_start: 0.5928 (mm) cc_final: 0.5545 (mm) REVERT: F 337 PHE cc_start: 0.6843 (t80) cc_final: 0.6557 (t80) REVERT: F 357 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6890 (p0) REVERT: F 367 TYR cc_start: 0.7350 (t80) cc_final: 0.7077 (t80) REVERT: F 415 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: F 490 GLN cc_start: 0.7428 (tp40) cc_final: 0.7178 (mm-40) REVERT: F 943 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7974 (mtpp) REVERT: F 1338 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: G 42 GLU cc_start: 0.6161 (pm20) cc_final: 0.5673 (tm-30) REVERT: G 78 LEU cc_start: 0.7020 (tm) cc_final: 0.6518 (pp) REVERT: G 87 LYS cc_start: 0.6909 (tttp) cc_final: 0.6300 (tptt) REVERT: G 164 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.6077 (mt0) REVERT: G 192 MET cc_start: 0.8412 (ptm) cc_final: 0.8129 (ptm) REVERT: G 204 GLU cc_start: 0.6501 (tt0) cc_final: 0.5840 (mt-10) REVERT: G 290 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6827 (tp) REVERT: G 371 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8044 (mtmm) REVERT: G 1205 GLU cc_start: 0.7432 (tt0) cc_final: 0.7127 (tt0) REVERT: G 1215 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: G 1291 GLU cc_start: 0.7233 (tp30) cc_final: 0.6970 (tp30) REVERT: G 1327 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8615 (mt-10) outliers start: 51 outliers final: 21 residues processed: 294 average time/residue: 0.8130 time to fit residues: 269.2217 Evaluate side-chains 294 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain E residue 193 GLU 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 415 GLU 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 164 GLN Chi-restraints excluded: chain G residue 290 ILE 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 931 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 254 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 277 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 628 HIS F1220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.145028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.090112 restraints weight = 58864.351| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.17 r_work: 0.2936 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 26339 Z= 0.253 Angle : 0.631 10.508 35798 Z= 0.333 Chirality : 0.047 0.216 4090 Planarity : 0.005 0.083 4511 Dihedral : 11.702 73.884 4062 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.15 % Allowed : 11.72 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.15), residues: 3150 helix: 1.06 (0.15), residues: 1133 sheet: -0.08 (0.24), residues: 401 loop : 0.00 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 143 TYR 0.021 0.002 TYR G 140 PHE 0.019 0.002 PHE F 337 TRP 0.019 0.002 TRP G1193 HIS 0.009 0.001 HIS F1023 Details of bonding type rmsd covalent geometry : bond 0.00597 (26331) covalent geometry : angle 0.62626 (35786) hydrogen bonds : bond 0.05050 ( 1138) hydrogen bonds : angle 5.05360 ( 3117) metal coordination : bond 0.00773 ( 8) metal coordination : angle 4.35351 ( 12) *********************** 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 329 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 18 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: E 58 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7836 (mt-10) REVERT: E 193 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: E 205 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8542 (ttt) REVERT: F 284 LEU cc_start: 0.5878 (mm) cc_final: 0.5450 (mm) REVERT: F 337 PHE cc_start: 0.7029 (t80) cc_final: 0.6760 (t80) REVERT: F 357 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6911 (p0) REVERT: F 367 TYR cc_start: 0.7415 (t80) cc_final: 0.7178 (t80) REVERT: F 490 GLN cc_start: 0.7465 (tp40) cc_final: 0.7196 (mm-40) REVERT: F 943 LYS cc_start: 0.8271 (mtmt) cc_final: 0.8017 (mtpp) REVERT: F 1338 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: G 78 LEU cc_start: 0.7047 (tm) cc_final: 0.6524 (pp) REVERT: G 87 LYS cc_start: 0.6935 (tttp) cc_final: 0.6294 (tptt) REVERT: G 164 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.6102 (mt0) REVERT: G 192 MET cc_start: 0.8401 (ptm) cc_final: 0.8101 (ptm) REVERT: G 204 GLU cc_start: 0.6543 (tt0) cc_final: 0.5884 (mt-10) REVERT: G 290 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6857 (tp) REVERT: G 371 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8089 (mtmm) REVERT: G 562 GLU cc_start: 0.7365 (mp0) cc_final: 0.7065 (pm20) REVERT: G 1205 GLU cc_start: 0.7437 (tt0) cc_final: 0.7172 (tt0) REVERT: G 1291 GLU cc_start: 0.7190 (tp30) cc_final: 0.6976 (tp30) REVERT: G 1298 VAL cc_start: 0.6874 (p) cc_final: 0.6527 (t) REVERT: G 1327 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8674 (mt-10) REVERT: G 1370 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7171 (mtm) outliers start: 58 outliers final: 26 residues processed: 311 average time/residue: 0.8353 time to fit residues: 292.8328 Evaluate side-chains 296 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 417 SER Chi-restraints excluded: chain F residue 633 LEU Chi-restraints excluded: chain F residue 634 VAL 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 164 GLN Chi-restraints excluded: chain G residue 290 ILE 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 812 ASP Chi-restraints excluded: chain G residue 931 THR 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 108 optimal weight: 3.9990 chunk 317 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 300 optimal weight: 6.9990 chunk 301 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 554 HIS F 618 GLN F 628 HIS G 708 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.147187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.093196 restraints weight = 54537.155| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.10 r_work: 0.2988 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26339 Z= 0.143 Angle : 0.542 8.923 35798 Z= 0.286 Chirality : 0.042 0.145 4090 Planarity : 0.005 0.067 4511 Dihedral : 11.496 73.662 4062 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 1.78 % Allowed : 12.90 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.15), residues: 3150 helix: 1.24 (0.15), residues: 1142 sheet: 0.01 (0.24), residues: 402 loop : 0.04 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 143 TYR 0.016 0.001 TYR G 140 PHE 0.016 0.001 PHE F 812 TRP 0.019 0.001 TRP G1193 HIS 0.005 0.001 HIS F1023 Details of bonding type rmsd covalent geometry : bond 0.00328 (26331) covalent geometry : angle 0.53835 (35786) hydrogen bonds : bond 0.04036 ( 1138) hydrogen bonds : angle 4.80990 ( 3117) metal coordination : bond 0.00569 ( 8) metal coordination : angle 3.66447 ( 12) *********************** 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 320 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 18 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: E 58 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7726 (mt-10) REVERT: E 193 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: E 205 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8593 (ttt) REVERT: F 218 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7475 (pp20) REVERT: F 284 LEU cc_start: 0.5942 (mm) cc_final: 0.5523 (mm) REVERT: F 337 PHE cc_start: 0.6935 (t80) cc_final: 0.6647 (t80) REVERT: F 367 TYR cc_start: 0.7392 (t80) cc_final: 0.7167 (t80) REVERT: F 415 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: F 434 ASP cc_start: 0.7613 (p0) cc_final: 0.6861 (m-30) REVERT: F 490 GLN cc_start: 0.7370 (tp40) cc_final: 0.7127 (mm-40) REVERT: F 943 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7976 (mtpp) REVERT: F 1338 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: G 78 LEU cc_start: 0.7036 (tm) cc_final: 0.6498 (pp) REVERT: G 87 LYS cc_start: 0.6972 (tttp) cc_final: 0.6316 (tptt) REVERT: G 192 MET cc_start: 0.8321 (ptm) cc_final: 0.7999 (ptm) REVERT: G 204 GLU cc_start: 0.6564 (tt0) cc_final: 0.5905 (mt-10) REVERT: G 290 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6789 (tp) REVERT: G 371 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8028 (mtmm) REVERT: G 1200 GLU cc_start: 0.5966 (mp0) cc_final: 0.4712 (tp30) REVERT: G 1205 GLU cc_start: 0.7480 (tt0) cc_final: 0.7163 (tt0) REVERT: G 1291 GLU cc_start: 0.7217 (tp30) cc_final: 0.6963 (tp30) REVERT: G 1327 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: G 1370 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7185 (mtm) outliers start: 48 outliers final: 22 residues processed: 303 average time/residue: 0.9045 time to fit residues: 307.5201 Evaluate side-chains 291 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 260 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 193 GLU 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 618 GLN 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 290 ILE Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 705 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 204 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.147069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092884 restraints weight = 56927.110| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.14 r_work: 0.2980 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26339 Z= 0.151 Angle : 0.550 8.965 35798 Z= 0.290 Chirality : 0.043 0.186 4090 Planarity : 0.005 0.086 4511 Dihedral : 11.480 73.713 4062 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Rotamer: Outliers : 1.48 % Allowed : 13.79 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 3150 helix: 1.28 (0.15), residues: 1142 sheet: -0.01 (0.24), residues: 402 loop : 0.05 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 143 TYR 0.016 0.001 TYR G 723 PHE 0.015 0.001 PHE G1319 TRP 0.017 0.001 TRP G1193 HIS 0.005 0.001 HIS F1023 Details of bonding type rmsd covalent geometry : bond 0.00348 (26331) covalent geometry : angle 0.54586 (35786) hydrogen bonds : bond 0.04116 ( 1138) hydrogen bonds : angle 4.78461 ( 3117) metal coordination : bond 0.00558 ( 8) metal coordination : angle 3.49998 ( 12) *********************** 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 305 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 18 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: E 58 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7644 (mt-10) REVERT: E 193 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: E 205 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8594 (ttt) REVERT: F 218 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7495 (pp20) REVERT: F 284 LEU cc_start: 0.5900 (mm) cc_final: 0.5474 (mm) REVERT: F 337 PHE cc_start: 0.6940 (t80) cc_final: 0.6640 (t80) REVERT: F 415 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: F 434 ASP cc_start: 0.7636 (p0) cc_final: 0.6856 (m-30) REVERT: F 490 GLN cc_start: 0.7390 (tp40) cc_final: 0.7147 (mm-40) REVERT: F 943 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7996 (mtpp) REVERT: F 1034 ARG cc_start: 0.7616 (mpp-170) cc_final: 0.7346 (mpp-170) REVERT: F 1338 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: G 78 LEU cc_start: 0.7025 (tm) cc_final: 0.6491 (pp) REVERT: G 87 LYS cc_start: 0.6992 (tttp) cc_final: 0.6345 (tptt) REVERT: G 155 GLU cc_start: 0.6049 (pm20) cc_final: 0.5822 (tm-30) REVERT: G 171 GLU cc_start: 0.6499 (tt0) cc_final: 0.6279 (pt0) REVERT: G 192 MET cc_start: 0.8297 (ptm) cc_final: 0.7997 (ptm) REVERT: G 204 GLU cc_start: 0.6569 (tt0) cc_final: 0.5899 (mt-10) REVERT: G 290 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6773 (tp) REVERT: G 371 LYS cc_start: 0.8430 (mtmm) cc_final: 0.7976 (mtmm) REVERT: G 1200 GLU cc_start: 0.5896 (mp0) cc_final: 0.4627 (tp30) REVERT: G 1205 GLU cc_start: 0.7431 (tt0) cc_final: 0.7113 (tt0) REVERT: G 1291 GLU cc_start: 0.7261 (tp30) cc_final: 0.6963 (tp30) REVERT: G 1327 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8525 (mt-10) REVERT: G 1370 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7169 (mtm) outliers start: 40 outliers final: 21 residues processed: 294 average time/residue: 0.9033 time to fit residues: 299.1181 Evaluate side-chains 292 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 262 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 193 GLU 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 618 GLN 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 290 ILE Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 705 THR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 200 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 F 955 GLN F1220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091817 restraints weight = 46965.854| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.97 r_work: 0.2955 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 26339 Z= 0.199 Angle : 0.589 9.296 35798 Z= 0.311 Chirality : 0.045 0.239 4090 Planarity : 0.005 0.098 4511 Dihedral : 11.563 73.791 4062 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 1.37 % Allowed : 14.13 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.15), residues: 3150 helix: 1.20 (0.15), residues: 1136 sheet: -0.06 (0.24), residues: 411 loop : 0.04 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 143 TYR 0.017 0.002 TYR G 140 PHE 0.015 0.002 PHE G1319 TRP 0.018 0.001 TRP G1193 HIS 0.007 0.001 HIS F1023 Details of bonding type rmsd covalent geometry : bond 0.00466 (26331) covalent geometry : angle 0.58539 (35786) hydrogen bonds : bond 0.04581 ( 1138) hydrogen bonds : angle 4.89828 ( 3117) metal coordination : bond 0.00630 ( 8) metal coordination : angle 3.75463 ( 12) *********************** 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 296 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 18 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: E 58 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7659 (mt-10) REVERT: E 193 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: E 205 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8535 (ttt) REVERT: F 201 ARG cc_start: 0.7137 (mtp180) cc_final: 0.6934 (mtp180) REVERT: F 218 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7456 (pp20) REVERT: F 284 LEU cc_start: 0.5823 (mm) cc_final: 0.5394 (mm) REVERT: F 337 PHE cc_start: 0.6971 (t80) cc_final: 0.6698 (t80) REVERT: F 415 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: F 490 GLN cc_start: 0.7394 (tp40) cc_final: 0.7134 (mm-40) REVERT: F 943 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7953 (mtpp) REVERT: F 1034 ARG cc_start: 0.7630 (mpp-170) cc_final: 0.7121 (tmt-80) REVERT: F 1338 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: G 78 LEU cc_start: 0.6954 (tm) cc_final: 0.6465 (pp) REVERT: G 87 LYS cc_start: 0.6992 (tttp) cc_final: 0.6337 (tptt) REVERT: G 192 MET cc_start: 0.8287 (ptm) cc_final: 0.7981 (ptm) REVERT: G 204 GLU cc_start: 0.6494 (tt0) cc_final: 0.5846 (mt-10) REVERT: G 290 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6849 (tp) REVERT: G 371 LYS cc_start: 0.8448 (mtmm) cc_final: 0.7979 (mtmm) REVERT: G 1200 GLU cc_start: 0.5959 (mp0) cc_final: 0.4579 (tp30) REVERT: G 1205 GLU cc_start: 0.7427 (tt0) cc_final: 0.7106 (tt0) REVERT: G 1215 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: G 1291 GLU cc_start: 0.7252 (tp30) cc_final: 0.6939 (tp30) REVERT: G 1327 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8538 (mt-10) REVERT: G 1370 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7141 (mtm) outliers start: 37 outliers final: 24 residues processed: 288 average time/residue: 0.7894 time to fit residues: 256.4282 Evaluate side-chains 289 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 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 386 GLU Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 705 THR 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 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 1370 MET 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 315 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 283 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 294 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.146804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.092788 restraints weight = 54391.051| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.09 r_work: 0.2979 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26339 Z= 0.159 Angle : 0.559 9.074 35798 Z= 0.295 Chirality : 0.043 0.242 4090 Planarity : 0.005 0.088 4511 Dihedral : 11.485 73.722 4062 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.29 % Favored : 97.68 % Rotamer: Outliers : 1.41 % Allowed : 14.28 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.15), residues: 3150 helix: 1.28 (0.15), residues: 1136 sheet: -0.07 (0.24), residues: 415 loop : 0.07 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 143 TYR 0.016 0.001 TYR G 723 PHE 0.015 0.002 PHE G1319 TRP 0.016 0.001 TRP G1193 HIS 0.005 0.001 HIS F1237 Details of bonding type rmsd covalent geometry : bond 0.00369 (26331) covalent geometry : angle 0.55552 (35786) hydrogen bonds : bond 0.04168 ( 1138) hydrogen bonds : angle 4.80317 ( 3117) metal coordination : bond 0.00566 ( 8) metal coordination : angle 3.54894 ( 12) ********************** 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 302 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 18 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: E 58 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7731 (mt-10) REVERT: E 93 GLN cc_start: 0.7297 (mp10) cc_final: 0.6949 (mp10) REVERT: E 193 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6075 (mp0) REVERT: E 205 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8593 (ttt) REVERT: F 218 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7484 (pp20) REVERT: F 284 LEU cc_start: 0.5851 (mm) cc_final: 0.5435 (mm) REVERT: F 337 PHE cc_start: 0.6964 (t80) cc_final: 0.6695 (t80) REVERT: F 357 ASN cc_start: 0.7206 (OUTLIER) cc_final: 0.6872 (p0) REVERT: F 415 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: F 434 ASP cc_start: 0.7630 (p0) cc_final: 0.6897 (m-30) REVERT: F 490 GLN cc_start: 0.7395 (tp40) cc_final: 0.7144 (mm-40) REVERT: F 943 LYS cc_start: 0.8237 (mtmt) cc_final: 0.8011 (mtpp) REVERT: F 1034 ARG cc_start: 0.7639 (mpp-170) cc_final: 0.7416 (mpp-170) REVERT: F 1338 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: G 78 LEU cc_start: 0.7024 (tm) cc_final: 0.6507 (pp) REVERT: G 87 LYS cc_start: 0.7044 (tttp) cc_final: 0.6357 (tptt) REVERT: G 155 GLU cc_start: 0.6413 (pm20) cc_final: 0.5918 (tm-30) REVERT: G 171 GLU cc_start: 0.6461 (tt0) cc_final: 0.6259 (pt0) REVERT: G 192 MET cc_start: 0.8298 (ptm) cc_final: 0.7992 (ptm) REVERT: G 204 GLU cc_start: 0.6546 (tt0) cc_final: 0.5906 (mt-10) REVERT: G 290 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6809 (tp) REVERT: G 371 LYS cc_start: 0.8433 (mtmm) cc_final: 0.7974 (mtmm) REVERT: G 1200 GLU cc_start: 0.5940 (mp0) cc_final: 0.4572 (tp30) REVERT: G 1205 GLU cc_start: 0.7439 (tt0) cc_final: 0.7151 (tt0) REVERT: G 1215 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: G 1291 GLU cc_start: 0.7269 (tp30) cc_final: 0.6976 (tp30) REVERT: G 1327 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: G 1370 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7183 (mtm) outliers start: 38 outliers final: 26 residues processed: 294 average time/residue: 0.8348 time to fit residues: 276.9794 Evaluate side-chains 295 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 441 GLU Chi-restraints excluded: chain F residue 618 GLN 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 386 GLU Chi-restraints excluded: chain G residue 499 ILE Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 663 GLU Chi-restraints excluded: chain G residue 705 THR 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 994 SER Chi-restraints excluded: chain G residue 1041 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 225 optimal weight: 0.0770 chunk 53 optimal weight: 0.0970 chunk 260 optimal weight: 7.9990 chunk 12 optimal weight: 0.2980 chunk 138 optimal weight: 8.9990 chunk 305 optimal weight: 0.8980 chunk 129 optimal weight: 0.0870 chunk 199 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 281 optimal weight: 8.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- 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 F 955 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.149412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096751 restraints weight = 56326.772| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.32 r_work: 0.3027 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 26339 Z= 0.101 Angle : 0.515 9.033 35798 Z= 0.270 Chirality : 0.041 0.183 4090 Planarity : 0.004 0.071 4511 Dihedral : 11.360 73.584 4062 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.20 % Favored : 97.77 % Rotamer: Outliers : 0.96 % Allowed : 14.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3150 helix: 1.45 (0.16), residues: 1137 sheet: 0.10 (0.24), residues: 410 loop : 0.14 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 143 TYR 0.013 0.001 TYR G 140 PHE 0.015 0.001 PHE G1319 TRP 0.014 0.001 TRP G1193 HIS 0.004 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00220 (26331) covalent geometry : angle 0.51172 (35786) hydrogen bonds : bond 0.03448 ( 1138) hydrogen bonds : angle 4.62271 ( 3117) metal coordination : bond 0.00435 ( 8) metal coordination : angle 3.11731 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15163.40 seconds wall clock time: 257 minutes 25.19 seconds (15445.19 seconds total)