Starting phenix.real_space_refine on Sat Jan 18 05:31:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xa8_38197/01_2025/8xa8_38197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xa8_38197/01_2025/8xa8_38197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xa8_38197/01_2025/8xa8_38197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xa8_38197/01_2025/8xa8_38197.map" model { file = "/net/cci-nas-00/data/ceres_data/8xa8_38197/01_2025/8xa8_38197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xa8_38197/01_2025/8xa8_38197.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 Mg 1 5.21 5 S 113 5.16 5 C 18350 2.51 5 N 5033 2.21 5 O 5492 1.98 5 H 28763 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 57754 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3387 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 9, 'TRANS': 214} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3273 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 18398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 18398 Classifications: {'peptide': 1184} Link IDs: {'PTRANS': 52, 'TRANS': 1131} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "E" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1113 Classifications: {'peptide': 69} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 960 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 12061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 12061 Classifications: {'peptide': 770} Link IDs: {'PTRANS': 21, 'TRANS': 748} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 145 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 18, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 116 Chain: "C" Number of atoms: 17056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 17056 Classifications: {'peptide': 1099} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1046} Chain breaks: 3 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1503 Classifications: {'peptide': 92} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7460 SG CYS D 60 127.282 29.710 71.655 1.00180.43 S ATOM 7487 SG CYS D 62 130.757 30.251 73.334 1.00194.66 S ATOM 7715 SG CYS D 75 128.253 27.631 74.675 1.00184.68 S ATOM 7761 SG CYS D 78 127.781 31.440 75.051 1.00192.01 S ATOM 19419 SG CYS D 818 64.903 28.352 86.631 1.00 75.95 S ATOM 20587 SG CYS D 892 65.842 31.832 85.558 1.00 68.47 S ATOM 20679 SG CYS D 899 64.526 29.253 82.965 1.00 63.61 S ATOM 20735 SG CYS D 902 62.214 30.832 85.405 1.00 72.86 S Time building chain proxies: 20.31, per 1000 atoms: 0.35 Number of scatterers: 57754 At special positions: 0 Unit cell: (144.4, 137.75, 168.15, 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 113 16.00 Mg 1 11.99 O 5492 8.00 N 5033 7.00 C 18350 6.00 H 28763 1.00 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: 11.91 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 902 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 899 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 892 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 818 " Number of angles added : 12 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 46 sheets defined 42.5% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 31 through 47 removed outlier: 3.527A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.870A pdb=" N ASN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 228 removed outlier: 4.324A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 removed outlier: 3.612A pdb=" N THR B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 205 through 226 removed outlier: 4.399A pdb=" N ILE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.634A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 170 through 181 removed outlier: 3.700A pdb=" N ALA D 174 " --> pdb=" O MET D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.727A pdb=" N ASP D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 219 removed outlier: 3.826A pdb=" N SER D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.639A pdb=" N ILE D 227 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 252 through 275 removed outlier: 3.994A pdb=" N ASP D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 removed outlier: 4.371A pdb=" N ASN D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 382 through 393 Processing helix chain 'D' and resid 394 through 397 Processing helix chain 'D' and resid 398 through 405 Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 440 through 444 removed outlier: 3.705A pdb=" N THR D 444 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 472 Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 493 through 504 removed outlier: 3.692A pdb=" N ASN D 499 " --> pdb=" O MET D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 563 through 569 Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 616 through 631 Processing helix chain 'D' and resid 632 through 655 Processing helix chain 'D' and resid 668 through 689 removed outlier: 3.518A pdb=" N GLU D 675 " --> pdb=" O GLU D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 720 removed outlier: 3.841A pdb=" N LYS D 718 " --> pdb=" O GLY D 714 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 720 " --> pdb=" O LEU D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 737 through 746 removed outlier: 4.277A pdb=" N GLN D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 781 Processing helix chain 'D' and resid 787 through 793 Processing helix chain 'D' and resid 798 through 809 Processing helix chain 'D' and resid 838 through 844 removed outlier: 3.731A pdb=" N ARG D 842 " --> pdb=" O ARG D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 879 removed outlier: 3.688A pdb=" N GLU D 875 " --> pdb=" O ASP D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 904 Processing helix chain 'D' and resid 918 through 938 Proline residue: D 930 - end of helix Processing helix chain 'D' and resid 940 through 945 removed outlier: 3.856A pdb=" N ALA D 945 " --> pdb=" O THR D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 961 Processing helix chain 'D' and resid 1030 through 1038 Processing helix chain 'D' and resid 1039 through 1058 Processing helix chain 'D' and resid 1063 through 1073 removed outlier: 3.705A pdb=" N VAL D1067 " --> pdb=" O GLY D1063 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1106 Processing helix chain 'D' and resid 1122 through 1129 Processing helix chain 'D' and resid 1132 through 1139 removed outlier: 3.561A pdb=" N SER D1138 " --> pdb=" O LEU D1134 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE D1139 " --> pdb=" O SER D1135 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1153 Processing helix chain 'D' and resid 1161 through 1168 Processing helix chain 'D' and resid 1173 through 1177 Processing helix chain 'D' and resid 1179 through 1183 removed outlier: 4.012A pdb=" N LYS D1182 " --> pdb=" O LYS D1179 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D1183 " --> pdb=" O TYR D1180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1179 through 1183' Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 29 through 38 Processing helix chain 'E' and resid 52 through 61 removed outlier: 3.537A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 61 " --> pdb=" O TYR E 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 removed outlier: 3.518A pdb=" N LEU F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 33 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'H' and resid 5 through 51 removed outlier: 3.886A pdb=" N LYS H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE H 28 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRP H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU H 49 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP H 50 " --> pdb=" O SER H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 98 removed outlier: 3.560A pdb=" N ARG H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 141 No H-bonds generated for 'chain 'H' and resid 139 through 141' Processing helix chain 'H' and resid 142 through 148 removed outlier: 3.746A pdb=" N TYR H 146 " --> pdb=" O SER H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 198 removed outlier: 3.650A pdb=" N LEU H 198 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 222 removed outlier: 4.638A pdb=" N ASP H 203 " --> pdb=" O SER H 199 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR H 204 " --> pdb=" O HIS H 200 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS H 207 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE H 220 " --> pdb=" O GLU H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 254 Processing helix chain 'H' and resid 259 through 261 No H-bonds generated for 'chain 'H' and resid 259 through 261' Processing helix chain 'H' and resid 270 through 280 removed outlier: 3.801A pdb=" N SER H 274 " --> pdb=" O PHE H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 302 Processing helix chain 'H' and resid 311 through 321 removed outlier: 4.033A pdb=" N GLU H 315 " --> pdb=" O PHE H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.601A pdb=" N ALA H 331 " --> pdb=" O PRO H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 337 Processing helix chain 'H' and resid 338 through 353 removed outlier: 3.724A pdb=" N GLN H 342 " --> pdb=" O GLY H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 382 Processing helix chain 'H' and resid 387 through 412 removed outlier: 3.894A pdb=" N LYS H 408 " --> pdb=" O ASN H 404 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS H 409 " --> pdb=" O LYS H 405 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG H 412 " --> pdb=" O LYS H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 421 removed outlier: 4.381A pdb=" N VAL H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 424 through 439 Processing helix chain 'H' and resid 447 through 474 Proline residue: H 467 - end of helix Processing helix chain 'H' and resid 479 through 486 Processing helix chain 'H' and resid 487 through 489 No H-bonds generated for 'chain 'H' and resid 487 through 489' Processing helix chain 'H' and resid 499 through 513 removed outlier: 3.610A pdb=" N ILE H 503 " --> pdb=" O LYS H 499 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 519 No H-bonds generated for 'chain 'H' and resid 517 through 519' Processing helix chain 'H' and resid 520 through 531 removed outlier: 3.666A pdb=" N PHE H 524 " --> pdb=" O ASP H 520 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU H 525 " --> pdb=" O ALA H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 551 Processing helix chain 'H' and resid 552 through 563 Processing helix chain 'H' and resid 584 through 589 removed outlier: 3.845A pdb=" N ARG H 588 " --> pdb=" O ASN H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 621 Processing helix chain 'H' and resid 646 through 650 Processing helix chain 'H' and resid 652 through 657 removed outlier: 3.660A pdb=" N GLY H 657 " --> pdb=" O ALA H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 657 through 663 Processing helix chain 'H' and resid 673 through 684 removed outlier: 3.989A pdb=" N CYS H 677 " --> pdb=" O THR H 673 " (cutoff:3.500A) Processing helix chain 'H' and resid 708 through 713 removed outlier: 3.750A pdb=" N LYS H 713 " --> pdb=" O VAL H 709 " (cutoff:3.500A) Processing helix chain 'H' and resid 727 through 731 removed outlier: 3.569A pdb=" N HIS H 731 " --> pdb=" O GLU H 728 " (cutoff:3.500A) Processing helix chain 'H' and resid 735 through 745 removed outlier: 4.173A pdb=" N LEU H 739 " --> pdb=" O ASP H 735 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 742 " --> pdb=" O LEU H 738 " (cutoff:3.500A) Processing helix chain 'H' and resid 759 through 764 Processing helix chain 'C' and resid 30 through 51 removed outlier: 4.012A pdb=" N SER C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 84 Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.556A pdb=" N LEU C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.708A pdb=" N ILE C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 224 Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'C' and resid 247 through 259 removed outlier: 4.093A pdb=" N SER C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 279 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 377 through 392 removed outlier: 3.516A pdb=" N ILE C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 438 removed outlier: 4.028A pdb=" N ILE C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 449 removed outlier: 3.766A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 464 removed outlier: 4.210A pdb=" N SER C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.814A pdb=" N TYR C 511 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 Processing helix chain 'C' and resid 604 through 608 removed outlier: 3.822A pdb=" N VAL C 608 " --> pdb=" O ARG C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.627A pdb=" N VAL C 619 " --> pdb=" O LYS C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 removed outlier: 3.852A pdb=" N ILE C 626 " --> pdb=" O THR C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 removed outlier: 4.032A pdb=" N MET C 639 " --> pdb=" O ASN C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 671 removed outlier: 4.259A pdb=" N VAL C 665 " --> pdb=" O GLY C 661 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY C 671 " --> pdb=" O GLY C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 697 No H-bonds generated for 'chain 'C' and resid 695 through 697' Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'C' and resid 817 through 822 Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 960 through 966 removed outlier: 4.547A pdb=" N SER C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 984 removed outlier: 3.993A pdb=" N VAL C 971 " --> pdb=" O ASN C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1008 Processing helix chain 'C' and resid 1043 through 1047 Processing helix chain 'C' and resid 1078 through 1087 Processing helix chain 'C' and resid 1088 through 1097 Processing helix chain 'C' and resid 1102 through 1116 Processing helix chain 'C' and resid 1125 through 1138 removed outlier: 3.788A pdb=" N LYS C1129 " --> pdb=" O PRO C1125 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 14 Processing helix chain 'I' and resid 15 through 28 Processing helix chain 'I' and resid 32 through 44 Processing helix chain 'I' and resid 53 through 65 Processing helix chain 'I' and resid 80 through 82 No H-bonds generated for 'chain 'I' and resid 80 through 82' Processing helix chain 'I' and resid 86 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 removed outlier: 5.213A pdb=" N ILE A 9 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU A 26 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR A 11 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 24 " --> pdb=" O THR A 11 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 194 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP A 192 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU A 29 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN A 190 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL A 185 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR A 191 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 6.357A pdb=" N ARG A 139 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE A 56 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR A 141 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12 removed outlier: 5.623A pdb=" N ASP B 192 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 53 Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 108 Processing sheet with id=AB2, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AB3, first strand: chain 'D' and resid 1155 through 1157 Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 96 Processing sheet with id=AB5, first strand: chain 'D' and resid 149 through 150 removed outlier: 6.754A pdb=" N GLN D 167 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 334 through 336 removed outlier: 3.510A pdb=" N GLN C1073 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 7.689A pdb=" N ILE D 436 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 343 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU D 438 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL D 345 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 515 through 516 Processing sheet with id=AB9, first strand: chain 'D' and resid 752 through 753 removed outlier: 3.710A pdb=" N ARG D 757 " --> pdb=" O ASN D 753 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 824 through 826 removed outlier: 4.548A pdb=" N PHE D 847 " --> pdb=" O ARG D 887 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 829 through 830 removed outlier: 6.767A pdb=" N LEU D 829 " --> pdb=" O ILE D 836 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 852 through 853 Processing sheet with id=AC4, first strand: chain 'D' and resid 977 through 983 removed outlier: 3.507A pdb=" N GLU D 983 " --> pdb=" O GLN D 988 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN D 988 " --> pdb=" O GLU D 983 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1093 through 1095 removed outlier: 4.503A pdb=" N LYS D1077 " --> pdb=" O VAL D1119 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 46 through 50 removed outlier: 4.090A pdb=" N ILE E 2 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N LEU E 67 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N TYR E 24 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 135 through 136 removed outlier: 7.484A pdb=" N TYR H 135 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR H 118 " --> pdb=" O TYR H 135 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG H 103 " --> pdb=" O LYS H 169 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS H 169 " --> pdb=" O ARG H 103 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP H 105 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 171 through 173 Processing sheet with id=AC9, first strand: chain 'H' and resid 289 through 290 removed outlier: 6.272A pdb=" N LEU H 229 " --> pdb=" O VAL H 570 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 362 through 364 removed outlier: 6.872A pdb=" N ILE H 362 " --> pdb=" O LEU H 369 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 703 through 706 removed outlier: 5.370A pdb=" N ILE H 667 " --> pdb=" O CYS H 705 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR H 666 " --> pdb=" O ALA H 719 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU H 721 " --> pdb=" O THR H 666 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA H 668 " --> pdb=" O LEU H 721 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TYR H 723 " --> pdb=" O ALA H 668 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE H 670 " --> pdb=" O TYR H 723 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASP H 718 " --> pdb=" O MET H 747 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET H 749 " --> pdb=" O ASP H 718 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 4 through 7 removed outlier: 7.526A pdb=" N ALA C 988 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.706A pdb=" N ILE C 55 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU C 64 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS C 95 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR C 69 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG C 93 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 71 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 114 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 94 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE C 112 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL C 96 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP C 110 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C 98 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP C 108 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN C 100 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL C 106 " --> pdb=" O ASN C 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AD6, first strand: chain 'C' and resid 137 through 140 Processing sheet with id=AD7, first strand: chain 'C' and resid 144 through 148 removed outlier: 4.840A pdb=" N PHE C 158 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 170 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 289 through 290 removed outlier: 4.299A pdb=" N ARG C 289 " --> pdb=" O PHE C 350 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 334 through 337 removed outlier: 3.545A pdb=" N VAL C 337 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AE2, first strand: chain 'C' and resid 536 through 537 removed outlier: 5.256A pdb=" N ARG C 560 " --> pdb=" O ARG C 549 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 600 through 603 Processing sheet with id=AE4, first strand: chain 'C' and resid 707 through 711 removed outlier: 4.239A pdb=" N ARG C 684 " --> pdb=" O TRP C 691 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG C 693 " --> pdb=" O VAL C 682 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL C 682 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY C 680 " --> pdb=" O VAL C 736 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.569A pdb=" N VAL C 716 " --> pdb=" O TYR C 724 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 727 through 728 Processing sheet with id=AE7, first strand: chain 'C' and resid 757 through 763 removed outlier: 3.586A pdb=" N ILE C 776 " --> pdb=" O MET C 956 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE C 775 " --> pdb=" O SER C 936 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE C 938 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET C 777 " --> pdb=" O ILE C 938 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER C1031 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 805 through 806 removed outlier: 6.591A pdb=" N ASP C 801 " --> pdb=" O VAL C 905 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 905 " --> pdb=" O ASP C 801 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN C 906 " --> pdb=" O ASN C 894 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN C 894 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 908 " --> pdb=" O VAL C 892 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 892 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG C 910 " --> pdb=" O VAL C 890 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL C 890 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR C 912 " --> pdb=" O HIS C 888 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 841 through 847 removed outlier: 3.655A pdb=" N VAL C 843 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 68 through 69 1259 hydrogen bonds defined for protein. 3513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.84 Time building geometry restraints manager: 14.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 28747 1.01 - 1.21: 24 1.21 - 1.42: 11875 1.42 - 1.62: 17419 1.62 - 1.82: 202 Bond restraints: 58267 Sorted by residual: bond pdb=" CA ARG D 414 " pdb=" C ARG D 414 " ideal model delta sigma weight residual 1.526 1.436 0.090 1.37e-02 5.33e+03 4.36e+01 bond pdb=" CA VAL A 25 " pdb=" C VAL A 25 " ideal model delta sigma weight residual 1.525 1.462 0.063 9.80e-03 1.04e+04 4.11e+01 bond pdb=" CA THR D 417 " pdb=" C THR D 417 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.04e-02 9.25e+03 3.42e+01 bond pdb=" NE ARG D 414 " pdb=" HE ARG D 414 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" NE ARG D 156 " pdb=" HE ARG D 156 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 58262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.84: 105461 10.84 - 21.68: 0 21.68 - 32.52: 4 32.52 - 43.36: 2 43.36 - 54.20: 2 Bond angle restraints: 105469 Sorted by residual: angle pdb=" C GLU E 68 " pdb=" N LEU E 69 " pdb=" H LEU E 69 " ideal model delta sigma weight residual 124.30 70.10 54.20 3.00e+00 1.11e-01 3.26e+02 angle pdb=" CA LEU E 69 " pdb=" N LEU E 69 " pdb=" H LEU E 69 " ideal model delta sigma weight residual 114.00 59.83 54.17 3.00e+00 1.11e-01 3.26e+02 angle pdb=" C VAL D1186 " pdb=" CA VAL D1186 " pdb=" HA VAL D1186 " ideal model delta sigma weight residual 109.00 74.51 34.49 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C GLN I 92 " pdb=" CA GLN I 92 " pdb=" HA GLN I 92 " ideal model delta sigma weight residual 109.00 76.39 32.61 3.00e+00 1.11e-01 1.18e+02 angle pdb=" N GLN I 92 " pdb=" CA GLN I 92 " pdb=" HA GLN I 92 " ideal model delta sigma weight residual 110.00 77.75 32.25 3.00e+00 1.11e-01 1.16e+02 ... (remaining 105464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 24805 25.15 - 50.30: 2010 50.30 - 75.45: 367 75.45 - 100.60: 69 100.60 - 125.75: 2 Dihedral angle restraints: 27253 sinusoidal: 14987 harmonic: 12266 Sorted by residual: dihedral pdb=" CA ALA D 415 " pdb=" C ALA D 415 " pdb=" N PRO D 416 " pdb=" CA PRO D 416 " ideal model delta harmonic sigma weight residual 180.00 54.25 125.75 0 5.00e+00 4.00e-02 6.33e+02 dihedral pdb=" CA GLU A 26 " pdb=" C GLU A 26 " pdb=" N PRO A 27 " pdb=" CA PRO A 27 " ideal model delta harmonic sigma weight residual -180.00 -61.61 -118.39 0 5.00e+00 4.00e-02 5.61e+02 dihedral pdb=" C VAL D1186 " pdb=" N VAL D1186 " pdb=" CA VAL D1186 " pdb=" CB VAL D1186 " ideal model delta harmonic sigma weight residual -122.00 -139.84 17.84 0 2.50e+00 1.60e-01 5.09e+01 ... (remaining 27250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 4490 0.119 - 0.239: 54 0.239 - 0.358: 0 0.358 - 0.477: 0 0.477 - 0.597: 2 Chirality restraints: 4546 Sorted by residual: chirality pdb=" CA GLN I 92 " pdb=" N GLN I 92 " pdb=" C GLN I 92 " pdb=" CB GLN I 92 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.91e+00 chirality pdb=" CA VAL D1186 " pdb=" N VAL D1186 " pdb=" C VAL D1186 " pdb=" CB VAL D1186 " both_signs ideal model delta sigma weight residual False 2.44 1.89 0.55 2.00e-01 2.50e+01 7.54e+00 chirality pdb=" CA ALA D 415 " pdb=" N ALA D 415 " pdb=" C ALA D 415 " pdb=" CB ALA D 415 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.17 2.00e-01 2.50e+01 7.66e-01 ... (remaining 4543 not shown) Planarity restraints: 8758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 810 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C ASP D 810 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP D 810 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL D 811 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 326 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO H 327 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 327 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 327 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 413 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C ASN D 413 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN D 413 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG D 414 " -0.010 2.00e-02 2.50e+03 ... (remaining 8755 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 1543 2.10 - 2.73: 104148 2.73 - 3.35: 174203 3.35 - 3.98: 220281 3.98 - 4.60: 345599 Nonbonded interactions: 845774 Sorted by model distance: nonbonded pdb=" OG1 THR D 652 " pdb=" H ASP C 767 " model vdw 1.477 2.450 nonbonded pdb=" O CYS D 75 " pdb=" H GLY D 79 " model vdw 1.567 2.450 nonbonded pdb=" H ASN C 538 " pdb=" O PHE C 542 " model vdw 1.577 2.450 nonbonded pdb=" H ILE D 559 " pdb=" O PHE D 594 " model vdw 1.581 2.450 nonbonded pdb=" OE1 GLU C 79 " pdb=" H GLU C 79 " model vdw 1.584 2.450 ... (remaining 845769 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 'A' and ((resid 5 through 6 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 7 through 12 or (resid 13 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 14 th \ rough 62 or (resid 63 through 64 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 65 through 68 or (resid 69 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 70 thr \ ough 87 or (resid 88 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 89 through 93 or (resid 94 through 95 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 96 thro \ ugh 101 or (resid 102 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 103 through 131 or (resid 132 through 133 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 13 \ 4 through 138 or (resid 139 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 140 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 158 or ( \ resid 159 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 160 through 228)) selection = (chain 'B' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 9 through 28 or (resid 29 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 30 through 228)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.800 Extract box with map and model: 1.750 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 115.750 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 0.090 29504 Z= 0.202 Angle : 0.528 9.202 39935 Z= 0.290 Chirality : 0.042 0.597 4546 Planarity : 0.003 0.049 5195 Dihedral : 18.438 125.752 11020 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.21 % Favored : 93.73 % Rotamer: Outliers : 0.49 % Allowed : 32.81 % Favored : 66.70 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3701 helix: 0.96 (0.15), residues: 1349 sheet: -0.62 (0.25), residues: 432 loop : -1.19 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 225 HIS 0.013 0.001 HIS D 94 PHE 0.009 0.001 PHE D 890 TYR 0.013 0.001 TYR D 650 ARG 0.006 0.000 ARG C 580 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 330 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 378 PRO cc_start: 0.7615 (Cg_exo) cc_final: 0.7247 (Cg_endo) outliers start: 15 outliers final: 11 residues processed: 342 average time/residue: 0.9093 time to fit residues: 494.6681 Evaluate side-chains 331 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 320 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 866 GLU Chi-restraints excluded: chain D residue 1132 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 620 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 289 optimal weight: 0.0060 chunk 111 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 335 optimal weight: 3.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN I 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.163597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125158 restraints weight = 120209.926| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.32 r_work: 0.3414 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29504 Z= 0.294 Angle : 0.560 17.273 39935 Z= 0.299 Chirality : 0.043 0.443 4546 Planarity : 0.005 0.119 5195 Dihedral : 5.472 93.843 4075 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 2.43 % Allowed : 30.84 % Favored : 66.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3701 helix: 0.85 (0.14), residues: 1394 sheet: -0.88 (0.24), residues: 445 loop : -1.27 (0.15), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 48 HIS 0.009 0.001 HIS D 94 PHE 0.014 0.001 PHE D1099 TYR 0.017 0.001 TYR C 695 ARG 0.006 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 413 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 338 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 821 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8205 (p0) REVERT: H 547 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7296 (mt-10) REVERT: C 341 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.6783 (mm-30) REVERT: C 378 PRO cc_start: 0.7766 (Cg_exo) cc_final: 0.7485 (Cg_endo) outliers start: 75 outliers final: 41 residues processed: 393 average time/residue: 0.8103 time to fit residues: 500.4773 Evaluate side-chains 367 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 324 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 751 MET Chi-restraints excluded: chain D residue 821 ASP Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1128 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 352 LEU Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 439 LYS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1056 TYR Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain I residue 88 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 340 optimal weight: 0.4980 chunk 330 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN D 951 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 HIS H 587 GLN ** C 482 HIS ** 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 = 0.4106 r_free = 0.4106 target = 0.164800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126173 restraints weight = 120064.170| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.39 r_work: 0.3422 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29504 Z= 0.230 Angle : 0.525 17.178 39935 Z= 0.278 Chirality : 0.042 0.454 4546 Planarity : 0.004 0.075 5195 Dihedral : 4.837 68.070 4059 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.48 % Favored : 93.41 % Rotamer: Outliers : 2.46 % Allowed : 30.29 % Favored : 67.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3701 helix: 0.91 (0.14), residues: 1397 sheet: -0.83 (0.25), residues: 434 loop : -1.30 (0.15), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 48 HIS 0.009 0.001 HIS D 94 PHE 0.012 0.001 PHE D1099 TYR 0.016 0.001 TYR D 650 ARG 0.017 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 341 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8925 (t) REVERT: B 182 ASN cc_start: 0.8294 (m-40) cc_final: 0.8080 (m-40) REVERT: D 338 TYR cc_start: 0.8142 (m-80) cc_final: 0.7858 (m-80) REVERT: D 442 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8491 (m) REVERT: D 497 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8321 (tt) REVERT: D 821 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8166 (p0) REVERT: D 1087 ASP cc_start: 0.6699 (t0) cc_final: 0.6374 (t0) REVERT: H 222 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7458 (mmt90) REVERT: H 547 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7183 (mt-10) REVERT: C 204 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: C 378 PRO cc_start: 0.7865 (Cg_exo) cc_final: 0.7664 (Cg_endo) outliers start: 76 outliers final: 48 residues processed: 404 average time/residue: 0.8017 time to fit residues: 508.7761 Evaluate side-chains 380 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 326 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 779 SER Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 821 ASP Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1128 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 503 ILE Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 595 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 929 HIS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1056 TYR Chi-restraints excluded: chain C residue 1127 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 75 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 206 optimal weight: 20.0000 chunk 280 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 240 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN D 5 ASN D 477 GLN D 951 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 HIS C 324 ASN ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125334 restraints weight = 120304.537| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.35 r_work: 0.3414 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29504 Z= 0.276 Angle : 0.534 17.327 39935 Z= 0.283 Chirality : 0.042 0.454 4546 Planarity : 0.004 0.073 5195 Dihedral : 4.852 66.694 4059 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.35 % Favored : 92.57 % Rotamer: Outliers : 3.02 % Allowed : 29.96 % Favored : 67.02 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3701 helix: 0.90 (0.14), residues: 1400 sheet: -0.99 (0.24), residues: 452 loop : -1.36 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 48 HIS 0.009 0.001 HIS D 94 PHE 0.012 0.001 PHE D1099 TYR 0.018 0.001 TYR D 650 ARG 0.006 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 426 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 333 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8926 (t) REVERT: D 338 TYR cc_start: 0.8372 (m-80) cc_final: 0.8029 (m-80) REVERT: D 497 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8301 (tt) REVERT: D 1012 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6927 (m) REVERT: H 222 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7437 (mmt180) REVERT: C 204 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: I 22 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7303 (tm-30) outliers start: 93 outliers final: 66 residues processed: 407 average time/residue: 0.8028 time to fit residues: 516.9046 Evaluate side-chains 389 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 317 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1128 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 494 LYS Chi-restraints excluded: chain H residue 503 ILE Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 689 ASN Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 890 VAL Chi-restraints excluded: chain C residue 929 HIS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1056 TYR Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 88 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 150 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 323 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 273 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN D 951 GLN H 386 HIS C 324 ASN ** C 482 HIS ** 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 = 0.4118 r_free = 0.4118 target = 0.166114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120940 restraints weight = 120984.220| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.49 r_work: 0.3425 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29504 Z= 0.252 Angle : 0.525 17.250 39935 Z= 0.278 Chirality : 0.042 0.454 4546 Planarity : 0.004 0.072 5195 Dihedral : 4.809 63.648 4059 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.67 % Favored : 93.25 % Rotamer: Outliers : 3.24 % Allowed : 29.80 % Favored : 66.96 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3701 helix: 0.94 (0.14), residues: 1394 sheet: -0.87 (0.24), residues: 435 loop : -1.35 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 48 HIS 0.010 0.001 HIS D 94 PHE 0.012 0.001 PHE D1099 TYR 0.017 0.001 TYR D 650 ARG 0.011 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 333 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8938 (t) REVERT: D 338 TYR cc_start: 0.8387 (m-80) cc_final: 0.7975 (m-80) REVERT: D 442 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8483 (m) REVERT: D 497 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8302 (tt) REVERT: D 821 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8216 (p0) REVERT: D 1087 ASP cc_start: 0.6760 (t0) cc_final: 0.6438 (t0) REVERT: F 44 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.7253 (m-70) REVERT: C 341 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6652 (mm-30) outliers start: 100 outliers final: 75 residues processed: 415 average time/residue: 0.8372 time to fit residues: 556.4817 Evaluate side-chains 402 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 321 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 821 ASP Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1128 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 455 LEU Chi-restraints excluded: chain H residue 494 LYS Chi-restraints excluded: chain H residue 503 ILE Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 747 MET Chi-restraints excluded: chain H residue 763 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 689 ASN Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 890 VAL Chi-restraints excluded: chain C residue 929 HIS Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1056 TYR Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain C residue 1141 ASP Chi-restraints excluded: chain I residue 88 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 248 optimal weight: 10.0000 chunk 302 optimal weight: 0.8980 chunk 306 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 335 optimal weight: 5.9990 chunk 350 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 344 optimal weight: 0.0570 chunk 179 optimal weight: 0.0870 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN H 386 HIS C 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.166561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127913 restraints weight = 119678.504| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.32 r_work: 0.3460 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29504 Z= 0.170 Angle : 0.503 17.657 39935 Z= 0.264 Chirality : 0.041 0.455 4546 Planarity : 0.004 0.070 5195 Dihedral : 4.650 62.005 4059 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 2.92 % Allowed : 30.19 % Favored : 66.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3701 helix: 1.09 (0.14), residues: 1395 sheet: -0.81 (0.25), residues: 429 loop : -1.29 (0.15), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 48 HIS 0.010 0.001 HIS D 94 PHE 0.014 0.001 PHE H 132 TYR 0.013 0.001 TYR D 650 ARG 0.008 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 349 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8908 (t) REVERT: A 187 GLN cc_start: 0.7805 (tp-100) cc_final: 0.7408 (tp-100) REVERT: A 194 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8821 (tp) REVERT: D 311 ARG cc_start: 0.7451 (ttp80) cc_final: 0.7248 (ttp80) REVERT: D 338 TYR cc_start: 0.8273 (m-80) cc_final: 0.7882 (m-80) REVERT: D 442 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8464 (m) REVERT: D 497 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8278 (tt) REVERT: D 821 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8166 (p0) REVERT: D 1012 VAL cc_start: 0.7145 (OUTLIER) cc_final: 0.6908 (m) REVERT: D 1087 ASP cc_start: 0.6637 (t0) cc_final: 0.6339 (t0) REVERT: F 44 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.7216 (m-70) REVERT: H 117 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7417 (mp) REVERT: H 222 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7392 (mmt90) REVERT: C 341 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6714 (mm-30) REVERT: I 22 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7191 (tm-30) outliers start: 90 outliers final: 67 residues processed: 423 average time/residue: 0.8407 time to fit residues: 562.8254 Evaluate side-chains 407 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 329 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 779 SER Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 821 ASP Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1128 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain H residue 219 GLN Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 455 LEU Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 499 LYS Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 747 MET Chi-restraints excluded: chain H residue 763 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 689 ASN Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 890 VAL Chi-restraints excluded: chain C residue 929 HIS Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1056 TYR Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain I residue 14 MET Chi-restraints excluded: chain I residue 22 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 302 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN H 386 HIS C 366 ASN ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.167007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126764 restraints weight = 120794.298| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.44 r_work: 0.3437 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29504 Z= 0.229 Angle : 0.515 17.396 39935 Z= 0.271 Chirality : 0.042 0.454 4546 Planarity : 0.004 0.070 5195 Dihedral : 4.664 61.692 4059 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.59 % Favored : 93.35 % Rotamer: Outliers : 3.15 % Allowed : 29.99 % Favored : 66.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3701 helix: 1.05 (0.14), residues: 1402 sheet: -0.82 (0.24), residues: 438 loop : -1.32 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 225 HIS 0.010 0.001 HIS D 94 PHE 0.011 0.001 PHE D1099 TYR 0.017 0.001 TYR C1086 ARG 0.008 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 429 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 332 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8925 (t) REVERT: A 187 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7438 (tp-100) REVERT: A 194 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8834 (tp) REVERT: D 311 ARG cc_start: 0.7499 (ttp80) cc_final: 0.7292 (ttp80) REVERT: D 338 TYR cc_start: 0.8361 (m-80) cc_final: 0.7953 (m-80) REVERT: D 442 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8481 (m) REVERT: D 497 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8263 (tt) REVERT: D 821 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8211 (p0) REVERT: D 1087 ASP cc_start: 0.6737 (t0) cc_final: 0.6528 (t0) REVERT: F 44 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7254 (m-70) REVERT: H 222 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7428 (mmt180) REVERT: C 341 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: I 22 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7172 (tm-30) outliers start: 97 outliers final: 79 residues processed: 413 average time/residue: 0.8047 time to fit residues: 525.9888 Evaluate side-chains 414 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 326 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 821 ASP Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1035 LEU Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1107 LEU Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1128 LEU Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 219 GLN Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 336 LYS Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 455 LEU Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 499 LYS Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 747 MET Chi-restraints excluded: chain H residue 763 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 689 ASN Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 890 VAL Chi-restraints excluded: chain C residue 929 HIS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1056 TYR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain I residue 22 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 206 optimal weight: 10.0000 chunk 368 optimal weight: 0.0970 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 275 optimal weight: 0.0040 chunk 280 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 303 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN H 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.167239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128689 restraints weight = 119766.160| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.29 r_work: 0.3464 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29504 Z= 0.156 Angle : 0.502 17.639 39935 Z= 0.263 Chirality : 0.041 0.454 4546 Planarity : 0.004 0.068 5195 Dihedral : 4.563 60.655 4059 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 2.95 % Allowed : 30.29 % Favored : 66.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3701 helix: 1.16 (0.14), residues: 1399 sheet: -0.76 (0.25), residues: 430 loop : -1.25 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 48 HIS 0.011 0.001 HIS D 94 PHE 0.009 0.001 PHE D1099 TYR 0.017 0.001 TYR C 181 ARG 0.007 0.000 ARG C 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 343 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.7787 (tp-100) cc_final: 0.7350 (tp-100) REVERT: A 194 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8832 (tp) REVERT: D 338 TYR cc_start: 0.8291 (m-80) cc_final: 0.7924 (m-80) REVERT: D 442 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8461 (m) REVERT: D 497 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8261 (tt) REVERT: D 821 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8187 (p0) REVERT: D 1012 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6911 (m) REVERT: F 44 HIS cc_start: 0.7459 (OUTLIER) cc_final: 0.7197 (m-70) REVERT: H 222 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7448 (mmt90) REVERT: H 443 GLU cc_start: 0.6813 (tp30) cc_final: 0.6521 (tp30) REVERT: C 205 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8080 (tm-30) REVERT: C 452 ARG cc_start: 0.7903 (tpt90) cc_final: 0.7631 (tpt170) REVERT: C 472 ASP cc_start: 0.7308 (p0) cc_final: 0.6967 (p0) REVERT: C 748 MET cc_start: 0.8160 (mtt) cc_final: 0.7890 (mtt) REVERT: I 22 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7213 (tm-30) outliers start: 91 outliers final: 71 residues processed: 420 average time/residue: 0.8193 time to fit residues: 544.2962 Evaluate side-chains 411 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 332 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 779 SER Chi-restraints excluded: chain D residue 821 ASP Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1128 LEU Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 219 GLN Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 336 LYS Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 374 GLN Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 455 LEU Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 499 LYS Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 747 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 689 ASN Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 890 VAL Chi-restraints excluded: chain C residue 929 HIS Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1056 TYR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain I residue 22 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 342 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 291 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 HIS C 366 ASN ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119937 restraints weight = 121193.489| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.57 r_work: 0.3401 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29504 Z= 0.336 Angle : 0.554 17.214 39935 Z= 0.294 Chirality : 0.043 0.450 4546 Planarity : 0.005 0.096 5195 Dihedral : 4.764 61.976 4059 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.43 % Favored : 92.52 % Rotamer: Outliers : 3.34 % Allowed : 30.06 % Favored : 66.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3701 helix: 1.00 (0.14), residues: 1399 sheet: -0.85 (0.24), residues: 435 loop : -1.39 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 225 HIS 0.009 0.001 HIS D 94 PHE 0.014 0.001 PHE D1099 TYR 0.020 0.001 TYR D 650 ARG 0.023 0.000 ARG D 311 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 435 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 332 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8867 (tp) REVERT: D 338 TYR cc_start: 0.8462 (m-80) cc_final: 0.8095 (m-80) REVERT: D 497 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8275 (tt) REVERT: D 821 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8278 (p0) REVERT: F 44 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.7236 (m-70) REVERT: H 222 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7461 (mmt180) REVERT: C 341 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: C 472 ASP cc_start: 0.7464 (p0) cc_final: 0.7100 (p0) REVERT: I 22 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7318 (tt0) outliers start: 103 outliers final: 83 residues processed: 416 average time/residue: 0.8167 time to fit residues: 539.5645 Evaluate side-chains 417 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 327 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 821 ASP Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1128 LEU Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 219 GLN Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 336 LYS Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 455 LEU Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 499 LYS Chi-restraints excluded: chain H residue 503 ILE Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 747 MET Chi-restraints excluded: chain H residue 763 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 890 VAL Chi-restraints excluded: chain C residue 929 HIS Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1056 TYR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain C residue 1141 ASP Chi-restraints excluded: chain I residue 22 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 279 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 199 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 HIS ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.163928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122073 restraints weight = 120412.700| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.45 r_work: 0.3426 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 29504 Z= 0.300 Angle : 0.662 59.013 39935 Z= 0.371 Chirality : 0.043 0.449 4546 Planarity : 0.005 0.116 5195 Dihedral : 4.767 61.922 4059 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 3.08 % Allowed : 30.45 % Favored : 66.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3701 helix: 0.99 (0.14), residues: 1399 sheet: -0.86 (0.24), residues: 435 loop : -1.39 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 691 HIS 0.010 0.001 HIS D 94 PHE 0.013 0.001 PHE D1099 TYR 0.020 0.001 TYR D 650 ARG 0.008 0.000 ARG D 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7402 Ramachandran restraints generated. 3701 Oldfield, 0 Emsley, 3701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LYS 6 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue THR 790 is missing expected H atoms. Skipping. Residue LYS 793 is missing expected H atoms. Skipping. Residue THR 794 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1184 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 304 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue LYS 463 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue LYS 536 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue LYS 263 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LYS 459 is missing expected H atoms. Skipping. Residue LYS 845 is missing expected H atoms. Skipping. Residue LYS 1067 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Evaluate side-chains 420 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 325 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8853 (tp) REVERT: D 338 TYR cc_start: 0.8417 (m-80) cc_final: 0.8031 (m-80) REVERT: D 497 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8247 (tt) REVERT: D 821 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8210 (p0) REVERT: F 44 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.7194 (m-70) REVERT: H 222 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7424 (mmt180) REVERT: C 341 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: C 472 ASP cc_start: 0.7406 (p0) cc_final: 0.7054 (p0) REVERT: I 22 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7339 (tt0) outliers start: 95 outliers final: 84 residues processed: 405 average time/residue: 0.8199 time to fit residues: 526.6189 Evaluate side-chains 416 residues out of total 3227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 325 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 569 GLU Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 608 GLN Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 682 ASN Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 821 ASP Chi-restraints excluded: chain D residue 844 ILE Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 921 ILE Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1128 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 219 GLN Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 336 LYS Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 422 LEU Chi-restraints excluded: chain H residue 455 LEU Chi-restraints excluded: chain H residue 489 SER Chi-restraints excluded: chain H residue 499 LYS Chi-restraints excluded: chain H residue 503 ILE Chi-restraints excluded: chain H residue 543 LEU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 717 PHE Chi-restraints excluded: chain H residue 747 MET Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 366 ASN Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 689 ASN Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 890 VAL Chi-restraints excluded: chain C residue 929 HIS Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain C residue 1056 TYR Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1127 SER Chi-restraints excluded: chain C residue 1141 ASP Chi-restraints excluded: chain I residue 22 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 362 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 360 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 951 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.164100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125449 restraints weight = 120360.314| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.39 r_work: 0.3420 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.322 29504 Z= 0.333 Angle : 0.711 59.188 39935 Z= 0.429 Chirality : 0.043 0.448 4546 Planarity : 0.005 0.150 5195 Dihedral : 4.774 61.922 4059 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.43 % Rotamer: Outliers : 3.15 % Allowed : 30.25 % Favored : 66.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3701 helix: 0.99 (0.14), residues: 1400 sheet: -0.86 (0.24), residues: 435 loop : -1.40 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 691 HIS 0.009 0.001 HIS D 94 PHE 0.013 0.001 PHE D1099 TYR 0.020 0.001 TYR D 650 ARG 0.006 0.000 ARG D 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26839.50 seconds wall clock time: 457 minutes 56.03 seconds (27476.03 seconds total)