Starting phenix.real_space_refine on Thu Jan 15 14:10:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pav_71446/01_2026/9pav_71446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pav_71446/01_2026/9pav_71446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pav_71446/01_2026/9pav_71446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pav_71446/01_2026/9pav_71446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pav_71446/01_2026/9pav_71446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pav_71446/01_2026/9pav_71446.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 71 5.16 5 C 16062 2.51 5 N 4546 2.21 5 O 4967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25647 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "L" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 2 Chain: "G" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "I" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 2 Chain: "A" Number of atoms: 10796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 10796 Classifications: {'peptide': 1472} Link IDs: {'PTRANS': 85, 'TRANS': 1386} Chain breaks: 1 Chain: "B" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8003 Classifications: {'peptide': 1090} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 59, 'TRANS': 1030} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 578 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.83, per 1000 atoms: 0.23 Number of scatterers: 25647 At special positions: 0 Unit cell: (125.4, 163.9, 205.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 1 15.00 O 4967 8.00 N 4546 7.00 C 16062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 39 " - pdb=" SG CYS L 109 " distance=2.03 Simple disulfide: pdb=" SG CYS L 156 " - pdb=" SG CYS L 216 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS I 39 " - pdb=" SG CYS I 109 " distance=2.04 Simple disulfide: pdb=" SG CYS I 156 " - pdb=" SG CYS I 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6252 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 40 sheets defined 34.8% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.508A pdb=" N THR H 95 " --> pdb=" O THR H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'L' and resid 100 through 104 removed outlier: 3.611A pdb=" N ASP L 103 " --> pdb=" O GLU L 100 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL L 104 " --> pdb=" O ALA L 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 104' Processing helix chain 'L' and resid 143 through 150 Processing helix chain 'L' and resid 205 through 211 removed outlier: 3.632A pdb=" N LYS L 210 " --> pdb=" O ALA L 206 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS L 211 " --> pdb=" O ASP L 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 34 removed outlier: 3.509A pdb=" N ASP G 33 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR G 34 " --> pdb=" O PHE G 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 30 through 34' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing helix chain 'I' and resid 100 through 104 removed outlier: 3.532A pdb=" N VAL I 104 " --> pdb=" O ALA I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 150 removed outlier: 3.569A pdb=" N SER I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 211 removed outlier: 3.860A pdb=" N HIS I 211 " --> pdb=" O ASP I 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 33 removed outlier: 3.889A pdb=" N LYS A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 15 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA A 16 " --> pdb=" O TYR A 12 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.846A pdb=" N ILE A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.691A pdb=" N VAL A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 180 through 191 removed outlier: 4.099A pdb=" N VAL A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 220 Processing helix chain 'A' and resid 236 through 246 removed outlier: 3.810A pdb=" N GLN A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 310 through 326 removed outlier: 3.590A pdb=" N GLN A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 removed outlier: 4.020A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.593A pdb=" N SER A 372 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 380 through 396 Processing helix chain 'A' and resid 477 through 494 removed outlier: 4.175A pdb=" N GLY A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 566 through 581 removed outlier: 3.563A pdb=" N ALA A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 600 through 622 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 633 through 636 Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 647 through 665 Processing helix chain 'A' and resid 678 through 685 removed outlier: 3.582A pdb=" N ARG A 685 " --> pdb=" O ASP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'A' and resid 735 through 740 removed outlier: 3.621A pdb=" N ASP A 740 " --> pdb=" O HIS A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 777 through 787 removed outlier: 3.612A pdb=" N TRP A 781 " --> pdb=" O ASP A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 801 Processing helix chain 'A' and resid 815 through 824 Processing helix chain 'A' and resid 836 through 851 removed outlier: 3.529A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.729A pdb=" N ALA A 858 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'A' and resid 925 through 941 removed outlier: 3.766A pdb=" N LEU A 929 " --> pdb=" O PRO A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1031 through 1044 removed outlier: 3.715A pdb=" N THR A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1130 through 1144 Processing helix chain 'A' and resid 1159 through 1176 Processing helix chain 'A' and resid 1187 through 1189 No H-bonds generated for 'chain 'A' and resid 1187 through 1189' Processing helix chain 'A' and resid 1190 through 1198 removed outlier: 3.841A pdb=" N GLY A1198 " --> pdb=" O VAL A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1252 Processing helix chain 'A' and resid 1267 through 1277 Processing helix chain 'A' and resid 1290 through 1300 removed outlier: 3.659A pdb=" N LEU A1294 " --> pdb=" O ASP A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1325 Processing helix chain 'A' and resid 1326 through 1335 removed outlier: 3.522A pdb=" N LEU A1330 " --> pdb=" O THR A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1348 Processing helix chain 'A' and resid 1362 through 1366 Processing helix chain 'A' and resid 1371 through 1391 Processing helix chain 'A' and resid 1408 through 1412 removed outlier: 4.438A pdb=" N HIS A1412 " --> pdb=" O MET A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1424 Processing helix chain 'A' and resid 1430 through 1445 Processing helix chain 'A' and resid 1454 through 1465 Processing helix chain 'A' and resid 1470 through 1474 removed outlier: 4.067A pdb=" N GLY A1474 " --> pdb=" O LEU A1471 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 33 removed outlier: 3.943A pdb=" N ALA B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 16 " --> pdb=" O TYR B 12 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 removed outlier: 3.568A pdb=" N GLU B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.588A pdb=" N ALA B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.600A pdb=" N ARG B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 191 removed outlier: 4.020A pdb=" N VAL B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 204 through 220 removed outlier: 3.605A pdb=" N VAL B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.576A pdb=" N GLN B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.642A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.608A pdb=" N ALA B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 removed outlier: 4.153A pdb=" N GLY B 416 " --> pdb=" O TRP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 493 Processing helix chain 'B' and resid 497 through 508 Processing helix chain 'B' and resid 522 through 533 Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 566 through 581 Processing helix chain 'B' and resid 582 through 584 No H-bonds generated for 'chain 'B' and resid 582 through 584' Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 600 through 623 Proline residue: B 606 - end of helix removed outlier: 3.890A pdb=" N GLY B 623 " --> pdb=" O TRP B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.520A pdb=" N ILE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 641 " --> pdb=" O ILE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 666 removed outlier: 4.564A pdb=" N LYS B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 685 removed outlier: 3.711A pdb=" N SER B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG B 685 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 719 Processing helix chain 'B' and resid 735 through 740 removed outlier: 3.672A pdb=" N VAL B 738 " --> pdb=" O THR B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 749 Processing helix chain 'B' and resid 777 through 787 Processing helix chain 'B' and resid 790 through 802 removed outlier: 3.977A pdb=" N ALA B 794 " --> pdb=" O ARG B 790 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 802 " --> pdb=" O LEU B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 824 removed outlier: 4.759A pdb=" N LEU B 819 " --> pdb=" O THR B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 850 removed outlier: 3.790A pdb=" N LEU B 840 " --> pdb=" O GLY B 836 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 859 removed outlier: 3.958A pdb=" N ALA B 858 " --> pdb=" O ASP B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 923 removed outlier: 3.537A pdb=" N GLY B 922 " --> pdb=" O ALA B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.672A pdb=" N LEU B 929 " --> pdb=" O PRO B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1031 through 1044 removed outlier: 3.634A pdb=" N VAL B1042 " --> pdb=" O ALA B1038 " (cutoff:3.500A) Processing helix chain 'C' and resid 1503 through 1518 Processing helix chain 'C' and resid 1530 through 1535 removed outlier: 3.617A pdb=" N GLY C1535 " --> pdb=" O PHE C1531 " (cutoff:3.500A) Processing helix chain 'C' and resid 1537 through 1553 removed outlier: 3.512A pdb=" N ALA C1551 " --> pdb=" O ARG C1547 " (cutoff:3.500A) Processing helix chain 'C' and resid 1559 through 1564 removed outlier: 3.902A pdb=" N ASP C1563 " --> pdb=" O ALA C1559 " (cutoff:3.500A) Processing helix chain 'C' and resid 1566 through 1576 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.732A pdb=" N THR H 73 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 12 through 14 removed outlier: 3.805A pdb=" N GLY H 12 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET H 36 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 12 through 14 removed outlier: 3.805A pdb=" N GLY H 12 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR H 109 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.747A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER H 187 " --> pdb=" O CYS H 147 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL H 188 " --> pdb=" O HIS H 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.747A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER H 187 " --> pdb=" O CYS H 147 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER H 184 " --> pdb=" O VAL H 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'L' and resid 35 through 39 Processing sheet with id=AA8, first strand: chain 'L' and resid 74 through 75 removed outlier: 6.535A pdb=" N TRP L 56 " --> pdb=" O LEU L 68 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR L 70 " --> pdb=" O LEU L 54 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU L 54 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY L 105 " --> pdb=" O VAL L 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 138 through 140 removed outlier: 4.132A pdb=" N VAL L 155 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER L 153 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU L 203 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL L 155 " --> pdb=" O LEU L 201 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU L 201 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU L 157 " --> pdb=" O SER L 199 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER L 199 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN L 159 " --> pdb=" O LEU L 197 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU L 197 " --> pdb=" O ASN L 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 167 through 170 removed outlier: 3.552A pdb=" N CYS L 216 " --> pdb=" O LYS L 229 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS L 229 " --> pdb=" O CYS L 216 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL L 227 " --> pdb=" O VAL L 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 5 through 9 removed outlier: 3.835A pdb=" N THR G 73 " --> pdb=" O GLN G 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'G' and resid 62 through 64 removed outlier: 6.811A pdb=" N TRP G 38 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE G 52 " --> pdb=" O MET G 36 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET G 36 " --> pdb=" O PHE G 52 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR G 109 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 62 through 64 removed outlier: 6.811A pdb=" N TRP G 38 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE G 52 " --> pdb=" O MET G 36 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET G 36 " --> pdb=" O PHE G 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 127 through 131 removed outlier: 4.815A pdb=" N GLY G 146 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL G 189 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU G 148 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER G 187 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS G 150 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU G 185 " --> pdb=" O LYS G 150 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER G 184 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA G 175 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER G 186 " --> pdb=" O PHE G 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 157 through 161 Processing sheet with id=AB8, first strand: chain 'I' and resid 21 through 22 Processing sheet with id=AB9, first strand: chain 'I' and resid 66 through 70 removed outlier: 6.708A pdb=" N TRP I 56 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR I 70 " --> pdb=" O LEU I 54 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU I 54 " --> pdb=" O TYR I 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 136 through 139 removed outlier: 3.533A pdb=" N ASN I 159 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER I 153 " --> pdb=" O LEU I 203 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU I 203 " --> pdb=" O SER I 153 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL I 155 " --> pdb=" O LEU I 201 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU I 201 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU I 157 " --> pdb=" O SER I 199 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N SER I 199 " --> pdb=" O LEU I 157 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASN I 159 " --> pdb=" O LEU I 197 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU I 197 " --> pdb=" O ASN I 159 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 167 through 170 removed outlier: 3.606A pdb=" N LYS I 229 " --> pdb=" O CYS I 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 418 through 420 removed outlier: 5.370A pdb=" N LEU A 365 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL A 334 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 447 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 297 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N HIS A 449 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER A 295 " --> pdb=" O HIS A 449 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 451 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 290 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 35 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 274 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N MET A 40 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 272 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS A 42 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 270 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 225 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 230 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 151 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL A 199 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 153 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR B 198 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 151 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL B 199 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER B 153 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY B 150 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N GLY B 228 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 152 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 230 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY B 154 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 225 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 270 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N CYS B 42 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 272 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET B 40 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 274 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 290 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 451 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER B 295 " --> pdb=" O HIS B 449 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N HIS B 449 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 297 " --> pdb=" O ASN B 447 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B 447 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 334 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 368 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AC5, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.624A pdb=" N ARG A 876 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AC7, first strand: chain 'A' and resid 469 through 475 Processing sheet with id=AC8, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.342A pdb=" N VAL A 544 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A 630 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TRP A 546 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 827 " --> pdb=" O PHE A 806 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 690 through 692 removed outlier: 3.648A pdb=" N VAL A 701 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 705 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 671 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET A 672 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 895 through 898 removed outlier: 3.548A pdb=" N ALA A 909 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 964 " --> pdb=" O ALA A 909 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG A 977 " --> pdb=" O THR A 997 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR A 997 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 979 " --> pdb=" O HIS A 995 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS A 995 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 981 " --> pdb=" O HIS A 993 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ALA A 999 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 945 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL A 944 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER A1056 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY A 946 " --> pdb=" O GLY A1054 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A1054 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG A1091 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TRP A1052 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N SER A1089 " --> pdb=" O TRP A1052 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY A1054 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A1087 " --> pdb=" O GLY A1054 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER A1056 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU A1085 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1065 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 923 through 924 removed outlier: 3.875A pdb=" N VAL A 954 " --> pdb=" O VAL A 924 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1213 through 1216 removed outlier: 4.756A pdb=" N VAL A1108 " --> pdb=" O THR A1447 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR A1447 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A1450 " --> pdb=" O ALA A1399 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE A1356 " --> pdb=" O VAL A1396 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE A1398 " --> pdb=" O PHE A1356 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A1358 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TRP A1400 " --> pdb=" O LEU A1358 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER A1360 " --> pdb=" O TRP A1400 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL A1357 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A1310 " --> pdb=" O VAL A1357 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE A1359 " --> pdb=" O VAL A1310 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N HIS A1312 " --> pdb=" O PHE A1359 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N SER A1361 " --> pdb=" O HIS A1312 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR A1231 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A1310 " --> pdb=" O THR A1231 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A1233 " --> pdb=" O VAL A1310 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N HIS A1312 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR A1235 " --> pdb=" O HIS A1312 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A1258 " --> pdb=" O ALA A1282 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ALA A1284 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A1260 " --> pdb=" O ALA A1284 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1112 through 1113 removed outlier: 4.068A pdb=" N ALA A1209 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL A1202 " --> pdb=" O ILE A1180 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A1182 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL A1204 " --> pdb=" O LEU A1182 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP A1184 " --> pdb=" O VAL A1204 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A1154 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A1185 " --> pdb=" O THR A1154 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A1124 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A1153 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR A1126 " --> pdb=" O VAL A1153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AD6, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AD7, first strand: chain 'B' and resid 397 through 398 removed outlier: 3.510A pdb=" N ARG B 425 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 469 through 475 Processing sheet with id=AD9, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.379A pdb=" N VAL B 545 " --> pdb=" O VAL B 807 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 690 through 692 removed outlier: 3.521A pdb=" N GLU B 691 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA B 704 " --> pdb=" O GLU B 691 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 761 through 763 removed outlier: 4.325A pdb=" N PHE B 761 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 895 through 898 removed outlier: 3.812A pdb=" N ALA B 994 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER B1050 " --> pdb=" O VAL B 950 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N THR B1093 " --> pdb=" O PRO B1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1015 through 1017 removed outlier: 3.560A pdb=" N VAL B1065 " --> pdb=" O VAL B1017 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B1074 " --> pdb=" O THR B1086 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N THR B1086 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B1076 " --> pdb=" O VAL B1084 " (cutoff:3.500A) 1133 hydrogen bonds defined for protein. 3102 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: 8.37 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8767 1.34 - 1.46: 5276 1.46 - 1.58: 11996 1.58 - 1.70: 3 1.70 - 1.82: 109 Bond restraints: 26151 Sorted by residual: bond pdb=" N VAL A 814 " pdb=" CA VAL A 814 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.17e+00 bond pdb=" N GLY B 631 " pdb=" CA GLY B 631 " ideal model delta sigma weight residual 1.445 1.473 -0.028 9.20e-03 1.18e+04 9.07e+00 bond pdb=" N ILE B 637 " pdb=" CA ILE B 637 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.02e+00 bond pdb=" N VAL A 816 " pdb=" CA VAL A 816 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.18e-02 7.18e+03 7.66e+00 bond pdb=" N VAL B 630 " pdb=" CA VAL B 630 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.50e+00 ... (remaining 26146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 35289 2.40 - 4.80: 352 4.80 - 7.20: 29 7.20 - 9.61: 7 9.61 - 12.01: 1 Bond angle restraints: 35678 Sorted by residual: angle pdb=" O HIS A 812 " pdb=" C HIS A 812 " pdb=" N PRO A 813 " ideal model delta sigma weight residual 121.84 117.24 4.60 7.80e-01 1.64e+00 3.48e+01 angle pdb=" N VAL B 177 " pdb=" CA VAL B 177 " pdb=" C VAL B 177 " ideal model delta sigma weight residual 113.53 108.76 4.77 9.80e-01 1.04e+00 2.36e+01 angle pdb=" C GLN B 378 " pdb=" CA GLN B 378 " pdb=" CB GLN B 378 " ideal model delta sigma weight residual 117.23 110.66 6.57 1.36e+00 5.41e-01 2.34e+01 angle pdb=" CA PRO B 813 " pdb=" N PRO B 813 " pdb=" CD PRO B 813 " ideal model delta sigma weight residual 112.00 106.16 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA MET A 672 " pdb=" CB MET A 672 " pdb=" CG MET A 672 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 ... (remaining 35673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13843 17.88 - 35.76: 1341 35.76 - 53.64: 327 53.64 - 71.52: 47 71.52 - 89.40: 36 Dihedral angle restraints: 15594 sinusoidal: 5828 harmonic: 9766 Sorted by residual: dihedral pdb=" CB CYS L 156 " pdb=" SG CYS L 156 " pdb=" SG CYS L 216 " pdb=" CB CYS L 216 " ideal model delta sinusoidal sigma weight residual 93.00 168.91 -75.91 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CA LEU B 13 " pdb=" C LEU B 13 " pdb=" N ARG B 14 " pdb=" CA ARG B 14 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASP H 151 " pdb=" CB ASP H 151 " pdb=" CG ASP H 151 " pdb=" OD1 ASP H 151 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 15591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3049 0.041 - 0.081: 728 0.081 - 0.122: 346 0.122 - 0.163: 18 0.163 - 0.203: 8 Chirality restraints: 4149 Sorted by residual: chirality pdb=" CB THR B 942 " pdb=" CA THR B 942 " pdb=" OG1 THR B 942 " pdb=" CG2 THR B 942 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU C1574 " pdb=" CB LEU C1574 " pdb=" CD1 LEU C1574 " pdb=" CD2 LEU C1574 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL B 655 " pdb=" N VAL B 655 " pdb=" C VAL B 655 " pdb=" CB VAL B 655 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 4146 not shown) Planarity restraints: 4684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 812 " -0.049 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO B 813 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 813 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 813 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 813 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.88e+00 pdb=" C PRO A 813 " 0.042 2.00e-02 2.50e+03 pdb=" O PRO A 813 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 814 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 697 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO A 698 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 698 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 698 " -0.032 5.00e-02 4.00e+02 ... (remaining 4681 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1954 2.74 - 3.28: 25592 3.28 - 3.82: 43056 3.82 - 4.36: 47904 4.36 - 4.90: 84138 Nonbonded interactions: 202644 Sorted by model distance: nonbonded pdb=" OG1 THR B 764 " pdb=" O ARG B 790 " model vdw 2.198 3.040 nonbonded pdb=" OE2 GLU B 679 " pdb=" NE2 GLN B 788 " model vdw 2.235 3.120 nonbonded pdb=" NZ LYS G 217 " pdb=" O VAL G 218 " model vdw 2.240 3.120 nonbonded pdb=" NE2 GLN A 215 " pdb=" OE1 GLN B 215 " model vdw 2.247 3.120 nonbonded pdb=" O LEU A 144 " pdb=" OG1 THR A 147 " model vdw 2.265 3.040 ... (remaining 202639 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 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } 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: 8.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.570 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 0.093 26157 Z= 0.147 Angle : 0.565 12.007 35690 Z= 0.309 Chirality : 0.042 0.203 4149 Planarity : 0.004 0.071 4684 Dihedral : 15.484 89.403 9324 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.49 % Allowed : 19.81 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3428 helix: 1.05 (0.17), residues: 1010 sheet: 0.09 (0.19), residues: 738 loop : -0.40 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 26 TYR 0.017 0.001 TYR A 731 PHE 0.010 0.001 PHE L 161 TRP 0.033 0.001 TRP A 546 HIS 0.005 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00263 (26151) covalent geometry : angle 0.56492 (35678) SS BOND : bond 0.00323 ( 6) SS BOND : angle 0.75482 ( 12) hydrogen bonds : bond 0.16232 ( 1105) hydrogen bonds : angle 6.78454 ( 3102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.911 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: C 1515 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8122 (mt-10) outliers start: 13 outliers final: 5 residues processed: 111 average time/residue: 0.1810 time to fit residues: 32.3075 Evaluate side-chains 94 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 630 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.101313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.066275 restraints weight = 120175.918| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 4.35 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26157 Z= 0.161 Angle : 0.554 7.814 35690 Z= 0.281 Chirality : 0.043 0.369 4149 Planarity : 0.004 0.045 4684 Dihedral : 4.487 62.268 3753 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.85 % Allowed : 18.27 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3428 helix: 1.39 (0.16), residues: 1036 sheet: 0.10 (0.19), residues: 749 loop : -0.42 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 572 TYR 0.009 0.001 TYR G 99 PHE 0.012 0.001 PHE L 161 TRP 0.035 0.001 TRP A 546 HIS 0.004 0.001 HIS B1031 Details of bonding type rmsd covalent geometry : bond 0.00373 (26151) covalent geometry : angle 0.55376 (35678) SS BOND : bond 0.00484 ( 6) SS BOND : angle 0.88998 ( 12) hydrogen bonds : bond 0.04159 ( 1105) hydrogen bonds : angle 5.14421 ( 3102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 101 time to evaluate : 0.992 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: A 12 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7979 (t80) REVERT: A 580 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6301 (mt) REVERT: A 630 VAL cc_start: 0.4786 (p) cc_final: 0.3651 (t) REVERT: B 672 MET cc_start: 0.5708 (mpp) cc_final: 0.5414 (mpp) REVERT: B 717 LEU cc_start: 0.8021 (mt) cc_final: 0.7736 (pp) REVERT: C 1515 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8043 (mt-10) outliers start: 76 outliers final: 33 residues processed: 164 average time/residue: 0.1687 time to fit residues: 45.1639 Evaluate side-chains 125 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 231 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1052 TRP Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 630 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 170 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 140 optimal weight: 0.3980 chunk 342 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 322 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 189 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.101542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066680 restraints weight = 120677.804| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.36 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26157 Z= 0.114 Angle : 0.505 7.167 35690 Z= 0.255 Chirality : 0.041 0.144 4149 Planarity : 0.004 0.057 4684 Dihedral : 4.253 59.716 3750 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.00 % Allowed : 18.08 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.15), residues: 3428 helix: 1.59 (0.17), residues: 1036 sheet: 0.11 (0.19), residues: 764 loop : -0.37 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 658 TYR 0.010 0.001 TYR A 782 PHE 0.024 0.001 PHE A 761 TRP 0.023 0.001 TRP A 546 HIS 0.003 0.001 HIS B1031 Details of bonding type rmsd covalent geometry : bond 0.00257 (26151) covalent geometry : angle 0.50528 (35678) SS BOND : bond 0.00380 ( 6) SS BOND : angle 0.76829 ( 12) hydrogen bonds : bond 0.03616 ( 1105) hydrogen bonds : angle 4.89099 ( 3102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 104 time to evaluate : 0.878 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: A 12 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7907 (t80) REVERT: A 276 GLU cc_start: 0.8291 (tp30) cc_final: 0.8075 (mm-30) REVERT: A 389 MET cc_start: 0.9629 (tpp) cc_final: 0.9407 (mmp) REVERT: A 420 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 558 MET cc_start: 0.5723 (mmm) cc_final: 0.5054 (mtt) REVERT: A 911 TRP cc_start: 0.5959 (m-90) cc_final: 0.5614 (m-90) REVERT: A 1180 ILE cc_start: 0.2103 (OUTLIER) cc_final: 0.1812 (mt) REVERT: B 672 MET cc_start: 0.5791 (mpp) cc_final: 0.5555 (mpp) REVERT: B 717 LEU cc_start: 0.8160 (mt) cc_final: 0.7887 (pp) REVERT: B 819 LEU cc_start: 0.8510 (tp) cc_final: 0.7968 (tp) REVERT: C 1515 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7941 (mt-10) outliers start: 80 outliers final: 45 residues processed: 174 average time/residue: 0.1526 time to fit residues: 44.1559 Evaluate side-chains 141 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 93 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 206 ASN Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 188 GLN Chi-restraints excluded: chain I residue 231 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1052 TRP Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain C residue 1560 MET Chi-restraints excluded: chain C residue 1563 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 2 optimal weight: 5.9990 chunk 196 optimal weight: 40.0000 chunk 323 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.098122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.059253 restraints weight = 115668.184| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.57 r_work: 0.2984 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26157 Z= 0.209 Angle : 0.614 9.631 35690 Z= 0.309 Chirality : 0.044 0.406 4149 Planarity : 0.005 0.049 4684 Dihedral : 4.589 61.424 3749 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.75 % Allowed : 17.71 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3428 helix: 1.39 (0.17), residues: 1027 sheet: 0.00 (0.19), residues: 760 loop : -0.50 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 244 TYR 0.028 0.002 TYR G 84 PHE 0.019 0.002 PHE A 761 TRP 0.031 0.001 TRP B1052 HIS 0.005 0.001 HIS B 737 Details of bonding type rmsd covalent geometry : bond 0.00484 (26151) covalent geometry : angle 0.61380 (35678) SS BOND : bond 0.00493 ( 6) SS BOND : angle 0.91518 ( 12) hydrogen bonds : bond 0.04576 ( 1105) hydrogen bonds : angle 5.07523 ( 3102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 97 time to evaluate : 0.878 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: L 217 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: I 81 ASP cc_start: 0.9459 (p0) cc_final: 0.9257 (p0) REVERT: I 98 ARG cc_start: 0.8378 (mtt-85) cc_final: 0.8151 (mmm160) REVERT: A 12 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8139 (t80) REVERT: A 336 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8569 (mt-10) REVERT: A 781 TRP cc_start: 0.6131 (m100) cc_final: 0.5485 (m100) REVERT: A 911 TRP cc_start: 0.3948 (m-90) cc_final: 0.3726 (m-90) REVERT: A 1349 ARG cc_start: 0.0609 (OUTLIER) cc_final: 0.0023 (ppt170) REVERT: B 287 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8634 (ptt90) REVERT: B 476 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.7651 (ttp-170) REVERT: B 717 LEU cc_start: 0.8388 (mt) cc_final: 0.8097 (tt) REVERT: C 1515 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8058 (mt-10) outliers start: 127 outliers final: 69 residues processed: 213 average time/residue: 0.1608 time to fit residues: 55.5830 Evaluate side-chains 163 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 88 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 217 GLU Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 231 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1454 ASP Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain C residue 1560 MET Chi-restraints excluded: chain C residue 1563 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 193 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 280 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 HIS ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.099461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.064391 restraints weight = 118802.255| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.32 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26157 Z= 0.110 Angle : 0.529 8.762 35690 Z= 0.263 Chirality : 0.042 0.257 4149 Planarity : 0.004 0.046 4684 Dihedral : 4.307 62.933 3749 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.73 % Allowed : 19.47 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 3428 helix: 1.61 (0.17), residues: 1020 sheet: 0.04 (0.19), residues: 763 loop : -0.42 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 244 TYR 0.012 0.001 TYR G 84 PHE 0.017 0.001 PHE A 548 TRP 0.019 0.001 TRP A 546 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00250 (26151) covalent geometry : angle 0.52931 (35678) SS BOND : bond 0.00333 ( 6) SS BOND : angle 0.74255 ( 12) hydrogen bonds : bond 0.03407 ( 1105) hydrogen bonds : angle 4.76814 ( 3102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 99 time to evaluate : 0.745 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: A 12 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7956 (t80) REVERT: A 336 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: A 389 MET cc_start: 0.9255 (tpp) cc_final: 0.8871 (tpp) REVERT: A 911 TRP cc_start: 0.5931 (m-90) cc_final: 0.5645 (m-90) REVERT: A 1349 ARG cc_start: -0.0205 (OUTLIER) cc_final: -0.0617 (ppt170) REVERT: B 287 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8513 (ptt90) REVERT: B 476 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8524 (mtt90) REVERT: B 717 LEU cc_start: 0.8258 (mt) cc_final: 0.8048 (tt) REVERT: B 816 VAL cc_start: 0.6458 (OUTLIER) cc_final: 0.4936 (p) REVERT: C 1515 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7904 (mt-10) outliers start: 73 outliers final: 46 residues processed: 165 average time/residue: 0.1731 time to fit residues: 45.1771 Evaluate side-chains 140 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 88 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 231 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1560 MET Chi-restraints excluded: chain C residue 1563 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 338 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 313 optimal weight: 0.0020 chunk 200 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 146 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1082 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.098680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.063621 restraints weight = 118941.734| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 4.31 r_work: 0.3029 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26157 Z= 0.137 Angle : 0.534 9.582 35690 Z= 0.266 Chirality : 0.042 0.213 4149 Planarity : 0.004 0.045 4684 Dihedral : 4.283 61.447 3749 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.56 % Allowed : 19.02 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 3428 helix: 1.66 (0.17), residues: 1031 sheet: 0.03 (0.18), residues: 772 loop : -0.41 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 572 TYR 0.011 0.001 TYR H 183 PHE 0.013 0.001 PHE A 242 TRP 0.025 0.001 TRP B1052 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00321 (26151) covalent geometry : angle 0.53376 (35678) SS BOND : bond 0.00455 ( 6) SS BOND : angle 0.88429 ( 12) hydrogen bonds : bond 0.03493 ( 1105) hydrogen bonds : angle 4.69217 ( 3102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 96 time to evaluate : 0.901 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: L 130 ARG cc_start: 0.4318 (ptm160) cc_final: 0.3247 (ttp-110) REVERT: A 12 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 336 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: A 389 MET cc_start: 0.9551 (tpp) cc_final: 0.9177 (tpp) REVERT: A 911 TRP cc_start: 0.5872 (m-90) cc_final: 0.5577 (m-90) REVERT: A 1349 ARG cc_start: -0.0155 (OUTLIER) cc_final: -0.0536 (ppt170) REVERT: B 287 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8526 (ptt90) REVERT: B 389 MET cc_start: 0.9600 (mmp) cc_final: 0.9395 (mmm) REVERT: B 476 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7547 (ttp-170) REVERT: B 717 LEU cc_start: 0.8295 (mt) cc_final: 0.8069 (tt) REVERT: C 1515 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8026 (mt-10) outliers start: 95 outliers final: 66 residues processed: 183 average time/residue: 0.1635 time to fit residues: 48.7797 Evaluate side-chains 159 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 88 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 231 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1454 ASP Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1560 MET Chi-restraints excluded: chain C residue 1563 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 206 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 274 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.098125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.063094 restraints weight = 118169.174| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.29 r_work: 0.3022 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26157 Z= 0.142 Angle : 0.544 9.802 35690 Z= 0.270 Chirality : 0.042 0.192 4149 Planarity : 0.004 0.045 4684 Dihedral : 4.308 61.465 3749 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.41 % Allowed : 19.24 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3428 helix: 1.69 (0.17), residues: 1036 sheet: 0.04 (0.18), residues: 786 loop : -0.43 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 625 TYR 0.013 0.001 TYR H 183 PHE 0.013 0.001 PHE A 242 TRP 0.030 0.001 TRP B1052 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00330 (26151) covalent geometry : angle 0.54350 (35678) SS BOND : bond 0.00377 ( 6) SS BOND : angle 0.93249 ( 12) hydrogen bonds : bond 0.03502 ( 1105) hydrogen bonds : angle 4.69070 ( 3102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 94 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8102 (t80) REVERT: A 336 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: A 389 MET cc_start: 0.9502 (tpp) cc_final: 0.9275 (tpp) REVERT: A 911 TRP cc_start: 0.5939 (m-90) cc_final: 0.5650 (m-90) REVERT: A 1349 ARG cc_start: -0.0139 (OUTLIER) cc_final: -0.0557 (ppt170) REVERT: B 287 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8515 (ptt90) REVERT: B 389 MET cc_start: 0.9609 (mmp) cc_final: 0.9384 (mmm) REVERT: B 476 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7624 (ttp-170) REVERT: B 672 MET cc_start: 0.5897 (mpp) cc_final: 0.3954 (tpp) REVERT: C 1515 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8128 (mt-10) outliers start: 91 outliers final: 69 residues processed: 176 average time/residue: 0.1679 time to fit residues: 48.2053 Evaluate side-chains 160 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 86 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 231 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1454 ASP Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1560 MET Chi-restraints excluded: chain C residue 1563 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 114 optimal weight: 0.8980 chunk 1 optimal weight: 0.0000 chunk 150 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.098649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.063576 restraints weight = 118017.594| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.37 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26157 Z= 0.100 Angle : 0.521 10.339 35690 Z= 0.256 Chirality : 0.042 0.200 4149 Planarity : 0.004 0.045 4684 Dihedral : 4.132 61.031 3749 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.81 % Allowed : 20.07 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3428 helix: 1.78 (0.17), residues: 1035 sheet: 0.10 (0.19), residues: 781 loop : -0.39 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 625 TYR 0.009 0.001 TYR B 878 PHE 0.011 0.001 PHE A 548 TRP 0.029 0.001 TRP B1052 HIS 0.005 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00230 (26151) covalent geometry : angle 0.52040 (35678) SS BOND : bond 0.00345 ( 6) SS BOND : angle 0.86158 ( 12) hydrogen bonds : bond 0.03047 ( 1105) hydrogen bonds : angle 4.52376 ( 3102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 97 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 103 ASP cc_start: 0.9026 (m-30) cc_final: 0.8739 (m-30) REVERT: A 12 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7884 (t80) REVERT: A 336 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: A 911 TRP cc_start: 0.5952 (m-90) cc_final: 0.5746 (m-90) REVERT: B 287 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8400 (ptt90) REVERT: B 389 MET cc_start: 0.9380 (mmp) cc_final: 0.9147 (mmm) REVERT: B 476 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8589 (mtt90) REVERT: C 1515 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7931 (mt-10) outliers start: 75 outliers final: 68 residues processed: 163 average time/residue: 0.1571 time to fit residues: 41.8964 Evaluate side-chains 159 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 87 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 231 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1454 ASP Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1560 MET Chi-restraints excluded: chain C residue 1563 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 0.0270 chunk 173 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 220 optimal weight: 0.5980 chunk 326 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 317 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 162 ASN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.097951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062961 restraints weight = 118258.898| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 4.29 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26157 Z= 0.119 Angle : 0.536 11.519 35690 Z= 0.263 Chirality : 0.042 0.184 4149 Planarity : 0.004 0.078 4684 Dihedral : 4.144 59.628 3749 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.11 % Allowed : 20.22 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 3428 helix: 1.81 (0.17), residues: 1038 sheet: 0.07 (0.19), residues: 784 loop : -0.33 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 84 TYR 0.024 0.001 TYR A 780 PHE 0.012 0.001 PHE A 242 TRP 0.032 0.001 TRP B1052 HIS 0.004 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00279 (26151) covalent geometry : angle 0.53541 (35678) SS BOND : bond 0.00377 ( 6) SS BOND : angle 0.91006 ( 12) hydrogen bonds : bond 0.03226 ( 1105) hydrogen bonds : angle 4.51893 ( 3102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 93 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 103 ASP cc_start: 0.9027 (m-30) cc_final: 0.8739 (m-30) REVERT: A 12 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7923 (t80) REVERT: A 336 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: A 1349 ARG cc_start: -0.0216 (OUTLIER) cc_final: -0.0516 (ppt170) REVERT: B 389 MET cc_start: 0.9391 (mmp) cc_final: 0.9175 (mmm) REVERT: B 476 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8613 (mtt90) REVERT: B 672 MET cc_start: 0.5604 (mpp) cc_final: 0.3821 (tpp) REVERT: C 1515 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7910 (mt-10) outliers start: 83 outliers final: 68 residues processed: 167 average time/residue: 0.1517 time to fit residues: 42.1535 Evaluate side-chains 160 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 88 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 231 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1454 ASP Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1560 MET Chi-restraints excluded: chain C residue 1563 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 277 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 185 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 chunk 337 optimal weight: 0.0030 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 52 optimal weight: 0.3980 overall best weight: 2.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1389 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 ASN C1573 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.101620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.068456 restraints weight = 123649.959| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 5.61 r_work: 0.2926 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26157 Z= 0.201 Angle : 0.632 11.435 35690 Z= 0.317 Chirality : 0.044 0.230 4149 Planarity : 0.005 0.052 4684 Dihedral : 4.715 59.958 3749 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.81 % Allowed : 20.63 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3428 helix: 1.56 (0.17), residues: 1032 sheet: -0.08 (0.18), residues: 788 loop : -0.49 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 244 TYR 0.014 0.002 TYR G 99 PHE 0.017 0.002 PHE A 609 TRP 0.040 0.002 TRP B1052 HIS 0.008 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00467 (26151) covalent geometry : angle 0.63214 (35678) SS BOND : bond 0.00478 ( 6) SS BOND : angle 1.31361 ( 12) hydrogen bonds : bond 0.04514 ( 1105) hydrogen bonds : angle 4.92443 ( 3102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 86 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 144 ASP cc_start: 0.8411 (p0) cc_final: 0.8077 (m-30) REVERT: G 18 ARG cc_start: 0.9018 (mmt180) cc_final: 0.8512 (mmt180) REVERT: A 12 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8172 (t80) REVERT: A 731 TYR cc_start: 0.7424 (p90) cc_final: 0.6987 (p90) REVERT: A 911 TRP cc_start: 0.4080 (m-90) cc_final: 0.3331 (m-90) REVERT: A 1349 ARG cc_start: 0.0518 (OUTLIER) cc_final: 0.0050 (ppt170) REVERT: B 287 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8598 (ptt90) REVERT: B 476 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.7824 (ttp-170) REVERT: B 672 MET cc_start: 0.5726 (mpp) cc_final: 0.3879 (tpp) REVERT: C 1515 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8174 (mt-10) outliers start: 75 outliers final: 65 residues processed: 154 average time/residue: 0.1632 time to fit residues: 41.1750 Evaluate side-chains 152 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 83 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain L residue 177 GLN Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 231 PHE Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 761 PHE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1349 ARG Chi-restraints excluded: chain A residue 1413 LEU Chi-restraints excluded: chain A residue 1454 ASP Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1563 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 10 optimal weight: 2.9990 chunk 289 optimal weight: 0.0270 chunk 210 optimal weight: 0.0970 chunk 137 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 242 optimal weight: 0.8980 chunk 179 optimal weight: 0.0020 chunk 25 optimal weight: 0.0370 chunk 273 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 GLN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.097978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.063113 restraints weight = 117263.966| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.23 r_work: 0.3039 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 26157 Z= 0.096 Angle : 0.545 11.440 35690 Z= 0.267 Chirality : 0.042 0.241 4149 Planarity : 0.004 0.044 4684 Dihedral : 4.264 60.585 3749 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.21 % Allowed : 21.08 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3428 helix: 1.76 (0.17), residues: 1037 sheet: 0.04 (0.19), residues: 781 loop : -0.35 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 84 TYR 0.019 0.001 TYR A 780 PHE 0.020 0.001 PHE A 548 TRP 0.030 0.001 TRP B1052 HIS 0.003 0.001 HIS A 993 Details of bonding type rmsd covalent geometry : bond 0.00219 (26151) covalent geometry : angle 0.54453 (35678) SS BOND : bond 0.00309 ( 6) SS BOND : angle 0.89425 ( 12) hydrogen bonds : bond 0.03022 ( 1105) hydrogen bonds : angle 4.54358 ( 3102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8474.41 seconds wall clock time: 144 minutes 58.98 seconds (8698.98 seconds total)