Starting phenix.real_space_refine on Sat Jul 4 22:13:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k17_61967/07_2026/9k17_61967.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k17_61967/07_2026/9k17_61967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k17_61967/07_2026/9k17_61967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k17_61967/07_2026/9k17_61967.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k17_61967/07_2026/9k17_61967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k17_61967/07_2026/9k17_61967.map" } resolution = 3.04 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 28 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14516 2.51 5 N 4037 2.21 5 O 4413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23142 Number of models: 1 Model: "" Number of chains: 18 Chain: "T" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain breaks: 1 Chain: "N" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 329 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain breaks: 1 Chain: "P" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 6608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6608 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 27, 'TRANS': 816} Chain breaks: 3 Chain: "C" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 1 Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 890 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "H" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain breaks: 1 Chain: "E" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1706 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain: "B" Number of atoms: 7660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7660 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 36, 'TRANS': 930} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5678 SG CYS A 989 15.115 72.601 32.117 1.00170.08 S ATOM 5785 SG CYS A1004 17.883 75.367 31.910 1.00146.97 S ATOM 7887 SG CYS C 90 81.623 39.728 135.334 1.00130.94 S ATOM 7906 SG CYS C 93 82.999 38.132 132.158 1.00136.25 S ATOM 7945 SG CYS C 99 82.036 35.818 134.971 1.00127.37 S ATOM 7971 SG CYS C 102 79.514 37.654 132.833 1.00112.99 S ATOM 10153 SG CYS J 7 51.631 40.236 116.582 1.00 59.40 S ATOM 10177 SG CYS J 10 50.987 41.043 120.273 1.00 61.55 S ATOM 10443 SG CYS J 44 48.459 42.131 117.501 1.00 64.67 S ATOM 10449 SG CYS J 45 48.915 38.536 118.731 1.00 67.29 S ATOM 11541 SG CYS L 12 79.900 14.791 89.521 1.00 89.21 S ATOM 11559 SG CYS L 15 79.700 11.402 90.952 1.00 99.25 S ATOM 11661 SG CYS L 29 82.594 12.395 88.546 1.00 95.79 S ATOM 11687 SG CYS L 32 78.855 11.591 87.504 1.00 98.03 S ATOM 13030 SG CYS I 7 25.184 45.874 18.471 1.00 60.99 S ATOM 13215 SG CYS I 29 29.269 47.426 17.691 1.00 66.58 S ATOM 13240 SG CYS I 32 27.619 45.498 15.544 1.00 52.81 S Time building chain proxies: 4.73, per 1000 atoms: 0.20 Number of scatterers: 23142 At special positions: 0 Unit cell: (114.975, 137.97, 162.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 141 16.00 P 28 15.00 Mg 1 11.99 O 4413 8.00 N 4037 7.00 C 14516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 940 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1004 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 989 " pdb=" ZN C 400 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 400 " - pdb=" SG CYS C 90 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " Number of angles added : 20 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5348 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 35 sheets defined 35.8% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 492 through 505 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.755A pdb=" N GLU A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 613 Proline residue: A 606 - end of helix removed outlier: 3.512A pdb=" N ASP A 613 " --> pdb=" O MET A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 removed outlier: 4.151A pdb=" N LEU A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 650 removed outlier: 4.830A pdb=" N SER A 643 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Proline residue: A 644 - end of helix removed outlier: 4.154A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 675 removed outlier: 3.879A pdb=" N ASN A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.739A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 750 through 771 Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.508A pdb=" N ALA A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 847 removed outlier: 3.668A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.591A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 891 through 904 Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.706A pdb=" N LEU A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.665A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.985A pdb=" N THR A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.939A pdb=" N VAL A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.684A pdb=" N ARG A1106 " --> pdb=" O ASP A1103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A1107 " --> pdb=" O THR A1104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1103 through 1107' Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1120 through 1138 removed outlier: 3.779A pdb=" N ALA A1124 " --> pdb=" O GLY A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 4.131A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1172 Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.701A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.718A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.780A pdb=" N ASP C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.747A pdb=" N SER C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 276 through 294 removed outlier: 3.625A pdb=" N VAL C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 Processing helix chain 'F' and resid 96 through 108 Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.746A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.765A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.949A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'E' and resid 30 through 51 removed outlier: 4.208A pdb=" N HIS E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 removed outlier: 3.765A pdb=" N PHE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.780A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.688A pdb=" N LEU E 137 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 156 removed outlier: 4.132A pdb=" N LEU E 156 " --> pdb=" O THR E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.575A pdb=" N GLN E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 21 through 40 Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.668A pdb=" N LEU B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 239 through 242 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 300 through 318 removed outlier: 3.802A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 360 through 380 Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 428 removed outlier: 3.788A pdb=" N VAL B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.599A pdb=" N THR B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.720A pdb=" N LEU B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 544 through 552 removed outlier: 3.621A pdb=" N LEU B 548 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 4.129A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.516A pdb=" N LYS B 635 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 632 through 636' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.589A pdb=" N GLU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 679 removed outlier: 3.829A pdb=" N GLN B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.606A pdb=" N LEU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.760A pdb=" N ASP B 706 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 717 Processing helix chain 'B' and resid 718 through 721 Processing helix chain 'B' and resid 729 through 733 removed outlier: 3.697A pdb=" N ILE B 732 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 733 " --> pdb=" O PRO B 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 729 through 733' Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 Processing helix chain 'B' and resid 943 through 945 No H-bonds generated for 'chain 'B' and resid 943 through 945' Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.546A pdb=" N ARG B 950 " --> pdb=" O ALA B 946 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 951' Processing helix chain 'B' and resid 953 through 966 Processing helix chain 'B' and resid 993 through 1004 Processing helix chain 'B' and resid 1040 through 1045 removed outlier: 3.613A pdb=" N LYS B1044 " --> pdb=" O MET B1040 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1040 through 1045' Processing sheet with id=AA1, first strand: chain 'B' and resid 1046 through 1048 removed outlier: 4.013A pdb=" N SER A 323 " --> pdb=" O ARG B1048 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 326 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 411 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL A 436 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 327 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE A 438 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR A 329 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.641A pdb=" N THR A 376 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG A 403 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N CYS A 372 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 375 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 377 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 531 removed outlier: 6.020A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 6.020A pdb=" N VAL A 529 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N HIS H 94 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 531 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N MET H 39 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR H 33 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL H 14 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP H 10 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG H 144 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 555 through 556 removed outlier: 6.326A pdb=" N ILE A 561 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AA8, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.986A pdb=" N VAL A 797 " --> pdb=" O VAL A 806 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1043 through 1049 removed outlier: 3.569A pdb=" N VAL A1071 " --> pdb=" O ILE A1049 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A1108 " --> pdb=" O ILE A 878 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 906 through 907 removed outlier: 7.101A pdb=" N VAL A 906 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 912 through 915 removed outlier: 7.162A pdb=" N HIS A 940 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 915 " --> pdb=" O HIS A 938 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HIS A 938 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 912 through 915 removed outlier: 7.162A pdb=" N HIS A 940 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 915 " --> pdb=" O HIS A 938 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HIS A 938 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 917 " --> pdb=" O TYR I 44 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR I 44 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR A 919 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N CYS I 42 " --> pdb=" O TYR A 919 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 3.529A pdb=" N GLU A1228 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1230 " --> pdb=" O THR F 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 18 removed outlier: 5.971A pdb=" N VAL C 12 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ARG C 27 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE C 14 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU C 25 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU C 190 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ASP C 263 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 11.208A pdb=" N MET C 188 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N PHE C 265 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N THR C 186 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N PHE C 267 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 11.256A pdb=" N THR C 184 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 10.135A pdb=" N VAL C 269 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N ALA C 182 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.215A pdb=" N GLU C 161 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL C 57 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LYS C 163 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE C 55 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG C 165 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL C 53 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 167 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL L 46 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.552A pdb=" N VAL C 154 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.573A pdb=" N ASP C 221 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.456A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 891 " --> pdb=" O ASN B 887 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.456A pdb=" N VAL B 882 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY B 877 " --> pdb=" O MET B 850 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 14 through 16 Processing sheet with id=AC4, first strand: chain 'I' and resid 86 through 89 Processing sheet with id=AC5, first strand: chain 'E' and resid 94 through 96 removed outlier: 6.400A pdb=" N LEU E 124 " --> pdb=" O GLU E 148 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE E 150 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU E 126 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 168 through 170 removed outlier: 3.590A pdb=" N ARG E 169 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E 212 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 225 " --> pdb=" O VAL E 213 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR E 223 " --> pdb=" O TYR E 215 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.715A pdb=" N MET B 68 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL B 89 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU B 133 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N PHE B 91 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 131 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 129 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA B 124 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG B 169 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET B 126 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC9, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AD1, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.451A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 225 through 226 Processing sheet with id=AD3, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AD4, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD5, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AD6, first strand: chain 'B' and resid 575 through 580 removed outlier: 7.149A pdb=" N VAL B 570 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL B 579 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N HIS B 568 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 6.876A pdb=" N ILE B 784 " --> pdb=" O TYR B 922 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLU B 924 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N MET B 786 " --> pdb=" O GLU B 924 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 855 through 857 removed outlier: 3.821A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) 866 hydrogen bonds defined for protein. 2421 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: 4.38 Time building geometry restraints manager: 2.40 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: 7542 1.34 - 1.46: 4389 1.46 - 1.58: 11405 1.58 - 1.70: 51 1.70 - 1.82: 217 Bond restraints: 23604 Sorted by residual: bond pdb=" C3' DT N 11 " pdb=" C2' DT N 11 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC N 18 " pdb=" C2' DC N 18 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.03e+00 bond pdb=" C1' DC N 14 " pdb=" N1 DC N 14 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.68e+00 bond pdb=" C3' DC N 14 " pdb=" C2' DC N 14 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.42e+00 bond pdb=" C1' DT N 11 " pdb=" N1 DT N 11 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.90e+00 ... (remaining 23599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 31666 2.62 - 5.24: 245 5.24 - 7.85: 25 7.85 - 10.47: 3 10.47 - 13.09: 1 Bond angle restraints: 31940 Sorted by residual: angle pdb=" CB MET H 39 " pdb=" CG MET H 39 " pdb=" SD MET H 39 " ideal model delta sigma weight residual 112.70 125.79 -13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" N3 DT N 15 " pdb=" C4 DT N 15 " pdb=" O4 DT N 15 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT T 5 " pdb=" C4 DT T 5 " pdb=" O4 DT T 5 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT N 28 " pdb=" C4 DT N 28 " pdb=" O4 DT N 28 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" C LYS B 827 " pdb=" N THR B 828 " pdb=" CA THR B 828 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.66e+01 ... (remaining 31935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 13782 34.86 - 69.72: 501 69.72 - 104.58: 31 104.58 - 139.44: 0 139.44 - 174.31: 1 Dihedral angle restraints: 14315 sinusoidal: 6059 harmonic: 8256 Sorted by residual: dihedral pdb=" CA GLN A 505 " pdb=" C GLN A 505 " pdb=" N VAL A 506 " pdb=" CA VAL A 506 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DC N 18 " pdb=" C3' DC N 18 " pdb=" O3' DC N 18 " pdb=" P DA N 19 " ideal model delta sinusoidal sigma weight residual -140.00 34.31 -174.31 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLN E 118 " pdb=" C GLN E 118 " pdb=" N GLU E 119 " pdb=" CA GLU E 119 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 14312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2388 0.035 - 0.070: 812 0.070 - 0.105: 292 0.105 - 0.141: 96 0.141 - 0.176: 5 Chirality restraints: 3593 Sorted by residual: chirality pdb=" CA LYS A 592 " pdb=" N LYS A 592 " pdb=" C LYS A 592 " pdb=" CB LYS A 592 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA GLU E 57 " pdb=" N GLU E 57 " pdb=" C GLU E 57 " pdb=" CB GLU E 57 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB ILE E 115 " pdb=" CA ILE E 115 " pdb=" CG1 ILE E 115 " pdb=" CG2 ILE E 115 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 3590 not shown) Planarity restraints: 4014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 229 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO B 230 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 101 " 0.016 2.00e-02 2.50e+03 1.52e-02 4.04e+00 pdb=" CG PHE C 101 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 101 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 101 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 101 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 101 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 101 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 127 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C VAL E 127 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL E 127 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU E 128 " 0.010 2.00e-02 2.50e+03 ... (remaining 4011 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 115 2.66 - 3.22: 20487 3.22 - 3.78: 33235 3.78 - 4.34: 45911 4.34 - 4.90: 75633 Nonbonded interactions: 175381 Sorted by model distance: nonbonded pdb=" OD1 ASP A 449 " pdb="MG MG A3000 " model vdw 2.100 2.170 nonbonded pdb=" N GLY I 82 " pdb="ZN ZN I 201 " model vdw 2.172 2.310 nonbonded pdb=" OD2 ASP A 449 " pdb="MG MG A3000 " model vdw 2.452 2.170 nonbonded pdb=" O LEU E 56 " pdb=" OE1 GLU E 57 " model vdw 2.489 3.040 nonbonded pdb=" O5' DT T 5 " pdb=" O4' DT T 5 " model vdw 2.501 2.432 ... (remaining 175376 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.230 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 0.041 23623 Z= 0.169 Angle : 0.665 13.090 31960 Z= 0.391 Chirality : 0.043 0.176 3593 Planarity : 0.004 0.053 4014 Dihedral : 17.073 174.306 8967 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.12 % Allowed : 17.01 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.15), residues: 2798 helix: 0.68 (0.18), residues: 860 sheet: -0.69 (0.23), residues: 485 loop : -1.72 (0.14), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1067 TYR 0.027 0.001 TYR E 202 PHE 0.035 0.001 PHE C 101 TRP 0.025 0.002 TRP A1050 HIS 0.002 0.001 HIS A 938 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.17 (23604) covalent geometry : angle 0.65513 / 0.39 (31940) hydrogen bonds : bond 0.20874 / 20.49 ( 855) hydrogen bonds : angle 6.72867 / 6.25 ( 2421) metal coordination : bond 0.00505 / 0.51 ( 19) metal coordination : angle 4.67888 / 7.29 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 779 PHE cc_start: 0.7906 (t80) cc_final: 0.7687 (t80) REVERT: A 953 MET cc_start: 0.6354 (pmm) cc_final: 0.6021 (pmm) REVERT: A 1006 MET cc_start: 0.8025 (mtm) cc_final: 0.7772 (mtp) REVERT: C 114 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8368 (m) REVERT: C 116 GLN cc_start: 0.8140 (mp10) cc_final: 0.7839 (pm20) REVERT: F 103 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7888 (tptp) REVERT: F 108 ARG cc_start: 0.7699 (ttp80) cc_final: 0.6931 (ptm160) REVERT: F 124 GLU cc_start: 0.7082 (tp30) cc_final: 0.6835 (tp30) REVERT: E 75 ASP cc_start: 0.4936 (p0) cc_final: 0.4731 (p0) REVERT: E 125 ILE cc_start: 0.3415 (mp) cc_final: 0.2601 (mp) REVERT: E 140 ILE cc_start: 0.7316 (mm) cc_final: 0.6805 (mm) REVERT: B 279 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8148 (t80) REVERT: B 422 MET cc_start: 0.8484 (ttm) cc_final: 0.8195 (ttp) REVERT: B 493 VAL cc_start: 0.8268 (p) cc_final: 0.8050 (m) REVERT: B 603 MET cc_start: 0.9327 (ttp) cc_final: 0.9055 (ttp) outliers start: 28 outliers final: 22 residues processed: 226 average time/residue: 0.1575 time to fit residues: 56.7137 Evaluate side-chains 194 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 837 SER Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 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 = 0.3894 r_free = 0.3894 target = 0.113935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.070796 restraints weight = 52934.217| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.74 r_work: 0.2929 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23623 Z= 0.159 Angle : 0.611 9.990 31960 Z= 0.323 Chirality : 0.043 0.172 3593 Planarity : 0.004 0.085 4014 Dihedral : 11.528 168.974 3435 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.87 % Allowed : 16.17 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.15), residues: 2798 helix: 0.75 (0.18), residues: 884 sheet: -0.55 (0.23), residues: 502 loop : -1.75 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 247 TYR 0.015 0.001 TYR B 235 PHE 0.029 0.002 PHE C 101 TRP 0.016 0.002 TRP A1050 HIS 0.004 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (23604) covalent geometry : angle 0.59925 / 0.32 (31940) hydrogen bonds : bond 0.05613 / 5.60 ( 855) hydrogen bonds : angle 5.16143 / 4.70 ( 2421) metal coordination : bond 0.00657 / 0.60 ( 19) metal coordination : angle 4.73982 / 7.35 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 179 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 953 MET cc_start: 0.6500 (pmm) cc_final: 0.6177 (pmm) REVERT: A 1006 MET cc_start: 0.7763 (mtm) cc_final: 0.7417 (mtp) REVERT: C 98 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: C 114 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8422 (p) REVERT: C 253 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8268 (tm-30) REVERT: F 99 GLU cc_start: 0.8810 (tp30) cc_final: 0.8599 (tp30) REVERT: F 102 MET cc_start: 0.7769 (mtm) cc_final: 0.7415 (mtm) REVERT: F 107 GLN cc_start: 0.8052 (mm110) cc_final: 0.7136 (mt0) REVERT: F 108 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7007 (ptm160) REVERT: F 124 GLU cc_start: 0.6981 (tp30) cc_final: 0.6465 (tp30) REVERT: H 52 MET cc_start: 0.7043 (ttm) cc_final: 0.6584 (ttm) REVERT: H 130 ILE cc_start: 0.6275 (mp) cc_final: 0.6018 (mt) REVERT: I 30 ARG cc_start: 0.6899 (mtt-85) cc_final: 0.6604 (mtp85) REVERT: E 218 GLU cc_start: 0.8113 (pp20) cc_final: 0.7340 (tm-30) REVERT: B 279 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8253 (t80) REVERT: B 340 PHE cc_start: 0.8652 (m-80) cc_final: 0.8444 (m-80) REVERT: B 422 MET cc_start: 0.8389 (ttm) cc_final: 0.7950 (ttp) REVERT: B 493 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8379 (m) REVERT: B 603 MET cc_start: 0.9147 (ttp) cc_final: 0.8792 (ttp) outliers start: 72 outliers final: 37 residues processed: 242 average time/residue: 0.1381 time to fit residues: 54.9400 Evaluate side-chains 211 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 160 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 34 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 181 optimal weight: 0.0570 chunk 222 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 overall best weight: 2.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 793 ASN ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN E 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.111055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.068529 restraints weight = 53332.221| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.01 r_work: 0.2862 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23623 Z= 0.207 Angle : 0.642 9.842 31960 Z= 0.339 Chirality : 0.045 0.212 3593 Planarity : 0.005 0.050 4014 Dihedral : 11.462 168.312 3418 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.74 % Allowed : 16.05 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.15), residues: 2798 helix: 0.73 (0.18), residues: 894 sheet: -0.54 (0.23), residues: 511 loop : -1.87 (0.15), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1067 TYR 0.015 0.002 TYR B 235 PHE 0.025 0.002 PHE C 101 TRP 0.013 0.002 TRP B 113 HIS 0.013 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (23604) covalent geometry : angle 0.63017 / 0.34 (31940) hydrogen bonds : bond 0.06029 / 6.05 ( 855) hydrogen bonds : angle 4.87791 / 4.48 ( 2421) metal coordination : bond 0.00688 / 0.69 ( 19) metal coordination : angle 4.94898 / 7.46 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 174 time to evaluate : 0.898 Fit side-chains REVERT: A 1098 VAL cc_start: 0.8149 (m) cc_final: 0.7940 (p) REVERT: C 98 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: C 253 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8346 (tm-30) REVERT: F 94 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: F 99 GLU cc_start: 0.8813 (tp30) cc_final: 0.8558 (tp30) REVERT: F 107 GLN cc_start: 0.7953 (mm110) cc_final: 0.6990 (mt0) REVERT: F 108 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7207 (ptm160) REVERT: F 124 GLU cc_start: 0.7146 (tp30) cc_final: 0.6712 (tp30) REVERT: H 52 MET cc_start: 0.7181 (ttm) cc_final: 0.6810 (ttm) REVERT: H 124 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5930 (ttm170) REVERT: H 130 ILE cc_start: 0.6196 (mp) cc_final: 0.5967 (mt) REVERT: I 30 ARG cc_start: 0.7155 (mtt-85) cc_final: 0.6526 (mtp85) REVERT: E 218 GLU cc_start: 0.7961 (pp20) cc_final: 0.7310 (tm-30) REVERT: B 279 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8084 (t80) REVERT: B 340 PHE cc_start: 0.8692 (m-80) cc_final: 0.8444 (m-80) REVERT: B 422 MET cc_start: 0.8468 (ttm) cc_final: 0.8011 (ttp) REVERT: B 493 VAL cc_start: 0.8654 (p) cc_final: 0.8385 (m) REVERT: B 603 MET cc_start: 0.9181 (ttp) cc_final: 0.8854 (ttp) outliers start: 94 outliers final: 58 residues processed: 248 average time/residue: 0.1322 time to fit residues: 54.2633 Evaluate side-chains 225 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 867 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 163 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 10 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.111213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.069106 restraints weight = 52978.662| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.97 r_work: 0.2876 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23623 Z= 0.146 Angle : 0.577 10.186 31960 Z= 0.302 Chirality : 0.043 0.182 3593 Planarity : 0.004 0.050 4014 Dihedral : 11.352 168.730 3416 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.11 % Allowed : 17.28 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.15), residues: 2798 helix: 0.88 (0.18), residues: 894 sheet: -0.51 (0.23), residues: 505 loop : -1.80 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1067 TYR 0.013 0.001 TYR J 43 PHE 0.021 0.001 PHE C 101 TRP 0.011 0.001 TRP B 113 HIS 0.004 0.001 HIS A 938 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (23604) covalent geometry : angle 0.56566 / 0.30 (31940) hydrogen bonds : bond 0.04902 / 4.97 ( 855) hydrogen bonds : angle 4.67631 / 4.27 ( 2421) metal coordination : bond 0.00587 / 0.59 ( 19) metal coordination : angle 4.68278 / 6.97 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 185 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1006 MET cc_start: 0.7843 (mtm) cc_final: 0.7469 (mtp) REVERT: A 1098 VAL cc_start: 0.8012 (m) cc_final: 0.7774 (p) REVERT: C 98 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: C 253 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8345 (tm-30) REVERT: F 94 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: F 107 GLN cc_start: 0.7937 (mm110) cc_final: 0.7149 (mt0) REVERT: F 108 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7507 (ptm160) REVERT: F 123 PHE cc_start: 0.7231 (p90) cc_final: 0.6958 (p90) REVERT: F 124 GLU cc_start: 0.7220 (tp30) cc_final: 0.6562 (tp30) REVERT: K 26 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8683 (mmtm) REVERT: H 52 MET cc_start: 0.7194 (ttm) cc_final: 0.6852 (ttm) REVERT: I 10 CYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7195 (t) REVERT: I 30 ARG cc_start: 0.7299 (mtt-85) cc_final: 0.6648 (mtp85) REVERT: E 57 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6998 (mm-30) REVERT: E 218 GLU cc_start: 0.8027 (pp20) cc_final: 0.7424 (tm-30) REVERT: B 279 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 340 PHE cc_start: 0.8729 (m-80) cc_final: 0.8472 (m-80) REVERT: B 422 MET cc_start: 0.8463 (ttm) cc_final: 0.8069 (ttp) REVERT: B 493 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8400 (m) REVERT: B 603 MET cc_start: 0.9209 (ttp) cc_final: 0.8903 (ttp) outliers start: 78 outliers final: 46 residues processed: 246 average time/residue: 0.1581 time to fit residues: 63.1047 Evaluate side-chains 222 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 867 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 261 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 201 optimal weight: 0.0070 chunk 270 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 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 = 0.3842 r_free = 0.3842 target = 0.110396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.068444 restraints weight = 52898.772| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.96 r_work: 0.2866 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23623 Z= 0.163 Angle : 0.590 9.748 31960 Z= 0.308 Chirality : 0.043 0.181 3593 Planarity : 0.004 0.049 4014 Dihedral : 11.323 168.092 3416 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.27 % Allowed : 17.28 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.15), residues: 2798 helix: 0.92 (0.18), residues: 893 sheet: -0.46 (0.23), residues: 505 loop : -1.81 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1067 TYR 0.014 0.001 TYR J 43 PHE 0.020 0.001 PHE C 101 TRP 0.011 0.001 TRP B 113 HIS 0.004 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (23604) covalent geometry : angle 0.57860 / 0.31 (31940) hydrogen bonds : bond 0.05029 / 5.10 ( 855) hydrogen bonds : angle 4.60521 / 4.21 ( 2421) metal coordination : bond 0.00584 / 0.59 ( 19) metal coordination : angle 4.59147 / 6.89 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 173 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1006 MET cc_start: 0.7966 (mtm) cc_final: 0.7541 (mtp) REVERT: C 98 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: C 116 GLN cc_start: 0.8265 (pm20) cc_final: 0.8045 (pm20) REVERT: C 200 MET cc_start: 0.7600 (tpt) cc_final: 0.7150 (tpp) REVERT: C 253 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8344 (tm-30) REVERT: F 94 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: F 107 GLN cc_start: 0.7929 (mm110) cc_final: 0.7253 (mt0) REVERT: F 108 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7615 (ptm160) REVERT: F 124 GLU cc_start: 0.7319 (tp30) cc_final: 0.6724 (tp30) REVERT: K 26 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8697 (mmtm) REVERT: H 52 MET cc_start: 0.7236 (ttm) cc_final: 0.6838 (ttm) REVERT: E 205 LEU cc_start: 0.5465 (OUTLIER) cc_final: 0.5222 (mt) REVERT: E 218 GLU cc_start: 0.8001 (pp20) cc_final: 0.7429 (tm-30) REVERT: B 340 PHE cc_start: 0.8755 (m-80) cc_final: 0.8505 (m-80) REVERT: B 422 MET cc_start: 0.8519 (ttm) cc_final: 0.8151 (ttp) REVERT: B 493 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8405 (m) REVERT: B 603 MET cc_start: 0.9209 (ttp) cc_final: 0.8922 (ttp) outliers start: 82 outliers final: 59 residues processed: 235 average time/residue: 0.1527 time to fit residues: 59.3131 Evaluate side-chains 228 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 165 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1116 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain B residue 1045 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 55 optimal weight: 7.9990 chunk 69 optimal weight: 0.0470 chunk 133 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 262 optimal weight: 9.9990 chunk 255 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 151 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 803 ASN ** H 42 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 = 0.3869 r_free = 0.3869 target = 0.112004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069938 restraints weight = 52914.862| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.05 r_work: 0.2898 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23623 Z= 0.101 Angle : 0.539 11.255 31960 Z= 0.280 Chirality : 0.041 0.168 3593 Planarity : 0.003 0.050 4014 Dihedral : 11.206 168.571 3415 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.35 % Allowed : 18.68 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.16), residues: 2798 helix: 1.10 (0.18), residues: 894 sheet: -0.39 (0.23), residues: 513 loop : -1.67 (0.15), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1067 TYR 0.013 0.001 TYR J 43 PHE 0.018 0.001 PHE C 101 TRP 0.011 0.001 TRP B 113 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (23604) covalent geometry : angle 0.52925 / 0.28 (31940) hydrogen bonds : bond 0.03933 / 4.04 ( 855) hydrogen bonds : angle 4.42060 / 4.02 ( 2421) metal coordination : bond 0.00519 / 0.47 ( 19) metal coordination : angle 4.18401 / 6.22 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 173 time to evaluate : 0.960 Fit side-chains REVERT: A 1006 MET cc_start: 0.7985 (mtm) cc_final: 0.7582 (mtp) REVERT: C 98 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: F 94 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: F 107 GLN cc_start: 0.8011 (mm110) cc_final: 0.7406 (mt0) REVERT: F 108 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7663 (ptm160) REVERT: F 123 PHE cc_start: 0.7255 (p90) cc_final: 0.6933 (p90) REVERT: F 124 GLU cc_start: 0.7259 (tp30) cc_final: 0.6472 (tp30) REVERT: K 26 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8671 (mmtm) REVERT: H 52 MET cc_start: 0.7194 (ttm) cc_final: 0.6818 (ttm) REVERT: E 205 LEU cc_start: 0.5409 (OUTLIER) cc_final: 0.5154 (mt) REVERT: E 218 GLU cc_start: 0.8012 (pp20) cc_final: 0.7438 (tm-30) REVERT: B 279 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8117 (t80) REVERT: B 340 PHE cc_start: 0.8802 (m-80) cc_final: 0.8543 (m-80) REVERT: B 422 MET cc_start: 0.8505 (ttm) cc_final: 0.8155 (ttp) REVERT: B 437 HIS cc_start: 0.7748 (m90) cc_final: 0.7535 (m90) REVERT: B 493 VAL cc_start: 0.8648 (p) cc_final: 0.8402 (m) REVERT: B 603 MET cc_start: 0.9194 (ttp) cc_final: 0.8920 (ttp) outliers start: 59 outliers final: 41 residues processed: 218 average time/residue: 0.1540 time to fit residues: 54.9998 Evaluate side-chains 213 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 129 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 256 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 950 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 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 = 0.3844 r_free = 0.3844 target = 0.110507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.068462 restraints weight = 52838.891| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.00 r_work: 0.2863 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23623 Z= 0.142 Angle : 0.567 10.525 31960 Z= 0.295 Chirality : 0.042 0.187 3593 Planarity : 0.004 0.050 4014 Dihedral : 11.194 167.615 3415 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.99 % Allowed : 18.44 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.16), residues: 2798 helix: 1.02 (0.18), residues: 907 sheet: -0.39 (0.23), residues: 511 loop : -1.72 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1067 TYR 0.013 0.001 TYR J 43 PHE 0.019 0.001 PHE C 101 TRP 0.011 0.001 TRP I 112 HIS 0.003 0.001 HIS I 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (23604) covalent geometry : angle 0.55675 / 0.29 (31940) hydrogen bonds : bond 0.04626 / 4.69 ( 855) hydrogen bonds : angle 4.43769 / 4.04 ( 2421) metal coordination : bond 0.00537 / 0.55 ( 19) metal coordination : angle 4.26639 / 6.47 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 174 time to evaluate : 1.028 Fit side-chains REVERT: A 459 TYR cc_start: 0.8182 (m-80) cc_final: 0.7898 (m-80) REVERT: A 1006 MET cc_start: 0.7996 (mtm) cc_final: 0.7571 (mtp) REVERT: C 98 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: C 116 GLN cc_start: 0.8281 (pm20) cc_final: 0.8061 (pm20) REVERT: C 200 MET cc_start: 0.7524 (tpt) cc_final: 0.7264 (tpp) REVERT: C 253 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8288 (tm-30) REVERT: F 94 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: F 107 GLN cc_start: 0.8074 (mm110) cc_final: 0.7471 (mt0) REVERT: F 108 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7654 (ttm-80) REVERT: F 123 PHE cc_start: 0.7301 (p90) cc_final: 0.6939 (p90) REVERT: F 124 GLU cc_start: 0.7348 (tp30) cc_final: 0.6530 (tp30) REVERT: F 137 TRP cc_start: 0.5823 (OUTLIER) cc_final: 0.5387 (m100) REVERT: K 26 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8683 (mmtm) REVERT: H 52 MET cc_start: 0.7244 (ttm) cc_final: 0.6845 (ttm) REVERT: E 205 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5619 (mt) REVERT: E 218 GLU cc_start: 0.8067 (pp20) cc_final: 0.7498 (tm-30) REVERT: B 340 PHE cc_start: 0.8805 (m-80) cc_final: 0.8550 (m-80) REVERT: B 422 MET cc_start: 0.8536 (ttm) cc_final: 0.8209 (ttp) REVERT: B 437 HIS cc_start: 0.7772 (m90) cc_final: 0.7514 (m90) REVERT: B 493 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8402 (m) REVERT: B 603 MET cc_start: 0.9210 (ttp) cc_final: 0.8910 (ttp) outliers start: 75 outliers final: 52 residues processed: 229 average time/residue: 0.1557 time to fit residues: 57.7964 Evaluate side-chains 216 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 1045 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 101 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 205 optimal weight: 0.4980 chunk 184 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 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 = 0.3855 r_free = 0.3855 target = 0.111154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.069346 restraints weight = 52497.417| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.95 r_work: 0.2888 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23623 Z= 0.108 Angle : 0.542 12.355 31960 Z= 0.280 Chirality : 0.042 0.167 3593 Planarity : 0.003 0.049 4014 Dihedral : 11.133 168.160 3415 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.27 % Allowed : 19.16 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.16), residues: 2798 helix: 1.16 (0.18), residues: 899 sheet: -0.36 (0.23), residues: 515 loop : -1.65 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1067 TYR 0.013 0.001 TYR J 43 PHE 0.017 0.001 PHE C 101 TRP 0.011 0.001 TRP B 113 HIS 0.004 0.001 HIS A 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (23604) covalent geometry : angle 0.53247 / 0.28 (31940) hydrogen bonds : bond 0.04014 / 4.12 ( 855) hydrogen bonds : angle 4.35958 / 3.96 ( 2421) metal coordination : bond 0.00476 / 0.45 ( 19) metal coordination : angle 4.09193 / 6.13 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 1.242 Fit side-chains REVERT: A 459 TYR cc_start: 0.8172 (m-80) cc_final: 0.7935 (m-80) REVERT: A 1006 MET cc_start: 0.7992 (mtm) cc_final: 0.7554 (mtp) REVERT: C 98 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: C 200 MET cc_start: 0.7549 (tpt) cc_final: 0.7307 (tpp) REVERT: F 94 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: F 107 GLN cc_start: 0.8061 (mm110) cc_final: 0.7497 (mt0) REVERT: F 108 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7756 (ttm-80) REVERT: F 123 PHE cc_start: 0.7421 (p90) cc_final: 0.7089 (p90) REVERT: F 124 GLU cc_start: 0.7295 (tp30) cc_final: 0.6473 (tp30) REVERT: F 137 TRP cc_start: 0.5736 (OUTLIER) cc_final: 0.5415 (m100) REVERT: K 26 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8661 (mmtm) REVERT: H 52 MET cc_start: 0.7209 (ttm) cc_final: 0.6875 (ttm) REVERT: H 131 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7847 (t) REVERT: E 205 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5861 (mt) REVERT: E 218 GLU cc_start: 0.8038 (pp20) cc_final: 0.7485 (tm-30) REVERT: B 340 PHE cc_start: 0.8826 (m-80) cc_final: 0.8609 (m-80) REVERT: B 422 MET cc_start: 0.8525 (ttm) cc_final: 0.8206 (ttp) REVERT: B 437 HIS cc_start: 0.7794 (m90) cc_final: 0.7528 (m90) REVERT: B 493 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8394 (m) REVERT: B 603 MET cc_start: 0.9189 (ttp) cc_final: 0.8897 (ttp) outliers start: 57 outliers final: 46 residues processed: 204 average time/residue: 0.1588 time to fit residues: 52.9967 Evaluate side-chains 210 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 235 optimal weight: 0.5980 chunk 262 optimal weight: 8.9990 chunk 265 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 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 = 0.3846 r_free = 0.3846 target = 0.110521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068472 restraints weight = 52818.908| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.74 r_work: 0.2891 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23623 Z= 0.121 Angle : 0.551 13.011 31960 Z= 0.284 Chirality : 0.042 0.167 3593 Planarity : 0.004 0.050 4014 Dihedral : 11.090 167.555 3414 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.31 % Allowed : 19.35 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.16), residues: 2798 helix: 1.15 (0.18), residues: 905 sheet: -0.37 (0.23), residues: 520 loop : -1.67 (0.15), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1067 TYR 0.013 0.001 TYR J 43 PHE 0.018 0.001 PHE C 101 TRP 0.010 0.001 TRP A1050 HIS 0.004 0.001 HIS A 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (23604) covalent geometry : angle 0.54144 / 0.28 (31940) hydrogen bonds : bond 0.04206 / 4.28 ( 855) hydrogen bonds : angle 4.33782 / 3.94 ( 2421) metal coordination : bond 0.00829 / 0.60 ( 19) metal coordination : angle 4.06696 / 6.09 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.921 Fit side-chains REVERT: A 459 TYR cc_start: 0.8175 (m-80) cc_final: 0.7965 (m-80) REVERT: A 856 GLU cc_start: 0.8825 (tp30) cc_final: 0.8422 (mt-10) REVERT: A 1006 MET cc_start: 0.8034 (mtm) cc_final: 0.7596 (mtp) REVERT: C 98 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: C 116 GLN cc_start: 0.8254 (pm20) cc_final: 0.8046 (pm20) REVERT: C 200 MET cc_start: 0.7638 (tpt) cc_final: 0.7409 (tpp) REVERT: F 94 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7390 (pm20) REVERT: F 107 GLN cc_start: 0.8061 (mm110) cc_final: 0.7419 (mt0) REVERT: F 108 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7735 (ttm-80) REVERT: F 124 GLU cc_start: 0.7257 (tp30) cc_final: 0.6541 (tp30) REVERT: F 137 TRP cc_start: 0.5731 (OUTLIER) cc_final: 0.5454 (m100) REVERT: K 26 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8672 (mmtm) REVERT: H 52 MET cc_start: 0.7235 (ttm) cc_final: 0.6915 (ttm) REVERT: H 131 SER cc_start: 0.8110 (OUTLIER) cc_final: 0.7827 (t) REVERT: E 205 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6069 (mt) REVERT: E 218 GLU cc_start: 0.7934 (pp20) cc_final: 0.7404 (tm-30) REVERT: B 340 PHE cc_start: 0.8851 (m-80) cc_final: 0.8645 (m-80) REVERT: B 422 MET cc_start: 0.8578 (ttm) cc_final: 0.8275 (ttp) REVERT: B 437 HIS cc_start: 0.7816 (m90) cc_final: 0.7541 (m90) REVERT: B 493 VAL cc_start: 0.8666 (p) cc_final: 0.8387 (m) REVERT: B 603 MET cc_start: 0.9154 (ttp) cc_final: 0.8861 (ttp) outliers start: 58 outliers final: 49 residues processed: 212 average time/residue: 0.1505 time to fit residues: 51.9387 Evaluate side-chains 216 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 100 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN ** B 824 GLN ** 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 = 0.3842 r_free = 0.3842 target = 0.110265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068635 restraints weight = 52706.955| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.91 r_work: 0.2873 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23623 Z= 0.126 Angle : 0.558 13.685 31960 Z= 0.287 Chirality : 0.042 0.166 3593 Planarity : 0.003 0.050 4014 Dihedral : 11.078 167.809 3414 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.39 % Allowed : 19.43 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.16), residues: 2798 helix: 1.16 (0.18), residues: 905 sheet: -0.39 (0.23), residues: 520 loop : -1.67 (0.15), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1067 TYR 0.013 0.001 TYR J 43 PHE 0.032 0.001 PHE C 101 TRP 0.010 0.001 TRP B 113 HIS 0.004 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (23604) covalent geometry : angle 0.54912 / 0.29 (31940) hydrogen bonds : bond 0.04200 / 4.29 ( 855) hydrogen bonds : angle 4.34136 / 3.94 ( 2421) metal coordination : bond 0.00493 / 0.50 ( 19) metal coordination : angle 4.04187 / 6.03 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 1.069 Fit side-chains REVERT: A 459 TYR cc_start: 0.8212 (m-80) cc_final: 0.7983 (m-80) REVERT: A 856 GLU cc_start: 0.8831 (tp30) cc_final: 0.8423 (mt-10) REVERT: A 1006 MET cc_start: 0.8011 (mtm) cc_final: 0.7547 (mtp) REVERT: C 98 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: C 200 MET cc_start: 0.7653 (tpt) cc_final: 0.7365 (tpp) REVERT: C 253 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8308 (tm-30) REVERT: F 63 LYS cc_start: 0.7539 (mmmt) cc_final: 0.7218 (ttpp) REVERT: F 94 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7404 (pm20) REVERT: F 107 GLN cc_start: 0.8090 (mm110) cc_final: 0.7450 (mt0) REVERT: F 108 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7774 (ttm-80) REVERT: F 123 PHE cc_start: 0.7651 (p90) cc_final: 0.7275 (p90) REVERT: F 124 GLU cc_start: 0.7277 (tp30) cc_final: 0.6445 (tp30) REVERT: F 137 TRP cc_start: 0.5760 (OUTLIER) cc_final: 0.5454 (m100) REVERT: J 1 MET cc_start: 0.9226 (mmt) cc_final: 0.8939 (mmt) REVERT: K 26 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8682 (mmtm) REVERT: H 52 MET cc_start: 0.7266 (ttm) cc_final: 0.6964 (ttm) REVERT: H 131 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7954 (t) REVERT: I 40 ASP cc_start: 0.5030 (OUTLIER) cc_final: 0.4630 (m-30) REVERT: E 205 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5994 (mt) REVERT: E 218 GLU cc_start: 0.7989 (pp20) cc_final: 0.7423 (tm-30) REVERT: B 340 PHE cc_start: 0.8887 (m-80) cc_final: 0.8664 (m-80) REVERT: B 422 MET cc_start: 0.8581 (ttm) cc_final: 0.8179 (ttp) REVERT: B 437 HIS cc_start: 0.7808 (m90) cc_final: 0.7523 (m90) REVERT: B 493 VAL cc_start: 0.8669 (p) cc_final: 0.8391 (m) REVERT: B 603 MET cc_start: 0.9205 (ttp) cc_final: 0.8915 (ttp) outliers start: 60 outliers final: 51 residues processed: 207 average time/residue: 0.1610 time to fit residues: 54.0181 Evaluate side-chains 216 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 670 TRP Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 985 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 199 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 232 optimal weight: 0.3980 chunk 209 optimal weight: 4.9990 chunk 273 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 127 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 HIS ** B 824 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 = 0.3859 r_free = 0.3859 target = 0.111038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.069538 restraints weight = 52536.633| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.71 r_work: 0.2920 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23623 Z= 0.099 Angle : 0.531 13.269 31960 Z= 0.273 Chirality : 0.041 0.164 3593 Planarity : 0.003 0.050 4014 Dihedral : 10.998 167.980 3414 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.23 % Allowed : 19.47 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.16), residues: 2798 helix: 1.34 (0.18), residues: 894 sheet: -0.29 (0.23), residues: 515 loop : -1.56 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 59 TYR 0.012 0.001 TYR J 43 PHE 0.035 0.001 PHE C 101 TRP 0.012 0.001 TRP B 113 HIS 0.003 0.001 HIS A 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (23604) covalent geometry : angle 0.52280 / 0.27 (31940) hydrogen bonds : bond 0.03555 / 3.67 ( 855) hydrogen bonds : angle 4.24257 / 3.85 ( 2421) metal coordination : bond 0.00521 / 0.43 ( 19) metal coordination : angle 3.80343 / 5.74 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6210.41 seconds wall clock time: 107 minutes 8.53 seconds (6428.53 seconds total)