Starting phenix.real_space_refine on Tue Sep 15 00:45:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vwy_32165/09_2026/7vwy_32165.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vwy_32165/09_2026/7vwy_32165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vwy_32165/09_2026/7vwy_32165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vwy_32165/09_2026/7vwy_32165.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vwy_32165/09_2026/7vwy_32165.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vwy_32165/09_2026/7vwy_32165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vwy_32165/09_2026/7vwy_32165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vwy_32165/09_2026/7vwy_32165.map" } resolution = 4.57 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 128 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 21330 2.51 5 N 6132 2.21 5 O 6894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34628 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2418 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10557 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 10391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10391 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1281} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3913 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "1" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1330 Classifications: {'DNA': 65} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 64} Chain: "2" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1324 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain: "G" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2298 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 17, 'TRANS': 265} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15200 SG CYS D 70 117.217 97.147 76.224 1.00 65.92 S ATOM 15214 SG CYS D 72 119.437 98.321 73.678 1.00 63.99 S ATOM 15346 SG CYS D 88 118.704 101.169 76.646 1.00 61.76 S ATOM 21032 SG CYS D 814 85.134 119.641 131.456 1.00 77.89 S ATOM 21597 SG CYS D 888 83.179 120.293 128.407 1.00 63.68 S ATOM 21648 SG CYS D 895 82.440 117.395 130.499 1.00 64.96 S ATOM 21669 SG CYS D 898 80.299 120.237 130.782 1.00 65.30 S Time building chain proxies: 6.89, per 1000 atoms: 0.20 Number of scatterers: 34628 At special positions: 0 Unit cell: (175.138, 207.813, 167.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 141 16.00 P 128 15.00 Mg 1 11.99 O 6894 8.00 N 6132 7.00 C 21330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7546 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 44 sheets defined 38.1% alpha, 10.3% beta 24 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.846A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.568A pdb=" N LEU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.758A pdb=" N ARG A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.971A pdb=" N LEU A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.716A pdb=" N GLU A 617 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 618 " --> pdb=" O GLU A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 618' Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.857A pdb=" N VAL A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.695A pdb=" N ASN B 41 " --> pdb=" O HIS B 37 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.801A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 removed outlier: 3.869A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.764A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 4.273A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.760A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.754A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.775A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 89 " --> pdb=" O CYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 4.057A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 221 removed outlier: 3.937A pdb=" N LEU C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.777A pdb=" N ARG C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.891A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 353 Processing helix chain 'C' and resid 362 through 371 removed outlier: 3.531A pdb=" N ILE C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.758A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.852A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 4.199A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 433 " --> pdb=" O MET C 429 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 435 " --> pdb=" O LYS C 431 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.994A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 4.520A pdb=" N ALA C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.753A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS C 526 " --> pdb=" O SER C 522 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.781A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.639A pdb=" N GLU C 611 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.730A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 685 through 689 removed outlier: 3.501A pdb=" N GLN C 688 " --> pdb=" O MET C 685 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 689 " --> pdb=" O GLN C 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 685 through 689' Processing helix chain 'C' and resid 704 through 709 removed outlier: 3.666A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 704 through 709' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 4.189A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 905 removed outlier: 3.886A pdb=" N LEU C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 4.126A pdb=" N LYS C 958 " --> pdb=" O LYS C 954 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 972 Processing helix chain 'C' and resid 973 through 975 No H-bonds generated for 'chain 'C' and resid 973 through 975' Processing helix chain 'C' and resid 977 through 981 removed outlier: 3.567A pdb=" N ALA C 981 " --> pdb=" O VAL C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 removed outlier: 3.510A pdb=" N LEU C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1011 removed outlier: 3.694A pdb=" N GLN C1010 " --> pdb=" O GLU C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1038 removed outlier: 4.020A pdb=" N TYR C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C1031 " --> pdb=" O LYS C1027 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C1034 " --> pdb=" O GLU C1030 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.440A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.511A pdb=" N ALA C1120 " --> pdb=" O HIS C1116 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY C1123 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1150 removed outlier: 3.587A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1170 Processing helix chain 'C' and resid 1171 through 1176 removed outlier: 3.519A pdb=" N ASN C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1199 removed outlier: 3.708A pdb=" N LEU C1199 " --> pdb=" O ILE C1195 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1280 Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 3.718A pdb=" N LEU C1291 " --> pdb=" O LEU C1287 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1310 removed outlier: 3.763A pdb=" N TYR C1305 " --> pdb=" O ARG C1301 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C1308 " --> pdb=" O MET C1304 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.802A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C1325 " --> pdb=" O GLU C1321 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C1329 " --> pdb=" O VAL C1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 34 removed outlier: 3.534A pdb=" N SER D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.556A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.707A pdb=" N ALA D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 189 Processing helix chain 'D' and resid 195 through 203 Processing helix chain 'D' and resid 203 through 208 removed outlier: 4.054A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 203 through 208' Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.470A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.538A pdb=" N ILE D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.568A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.586A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.665A pdb=" N GLN D 335 " --> pdb=" O LYS D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.875A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 393 through 398 Processing helix chain 'D' and resid 399 through 401 No H-bonds generated for 'chain 'D' and resid 399 through 401' Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.518A pdb=" N VAL D 415 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 454 removed outlier: 3.572A pdb=" N VAL D 453 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS D 454 " --> pdb=" O PRO D 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 450 through 454' Processing helix chain 'D' and resid 473 through 481 removed outlier: 3.875A pdb=" N ARG D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.721A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.838A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 removed outlier: 3.654A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 597 through 605 removed outlier: 3.627A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 612 removed outlier: 3.642A pdb=" N ILE D 611 " --> pdb=" O THR D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 629 removed outlier: 3.636A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 634 removed outlier: 3.765A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 670 removed outlier: 3.536A pdb=" N GLU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 700 removed outlier: 4.788A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET D 698 " --> pdb=" O SER D 694 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 727 removed outlier: 3.527A pdb=" N ALA D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 739 removed outlier: 3.501A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 774 Processing helix chain 'D' and resid 775 through 804 removed outlier: 3.869A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.816A pdb=" N VAL D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 4.455A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 914 through 923 Processing helix chain 'D' and resid 925 through 930 removed outlier: 3.799A pdb=" N THR D 928 " --> pdb=" O GLU D 925 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN D 929 " --> pdb=" O PRO D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1147 removed outlier: 3.643A pdb=" N ALA D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP D1143 " --> pdb=" O PRO D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1242 removed outlier: 3.518A pdb=" N THR D1230 " --> pdb=" O VAL D1226 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D1236 " --> pdb=" O TYR D1232 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D1242 " --> pdb=" O GLN D1238 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1255 removed outlier: 3.590A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1288 removed outlier: 3.704A pdb=" N LYS D1286 " --> pdb=" O TYR D1282 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D1287 " --> pdb=" O SER D1283 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1329 through 1337 removed outlier: 3.550A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 removed outlier: 3.754A pdb=" N ILE D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1348 through 1353' Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1374 removed outlier: 3.764A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.517A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 30 removed outlier: 4.055A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 56 removed outlier: 3.721A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 79 removed outlier: 3.773A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.548A pdb=" N MET F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET F 105 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 135 removed outlier: 3.641A pdb=" N ILE F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 144 removed outlier: 4.085A pdb=" N LEU F 144 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 151 Processing helix chain 'F' and resid 159 through 165 removed outlier: 3.839A pdb=" N THR F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 227 removed outlier: 4.203A pdb=" N ALA F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 237 removed outlier: 3.521A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 4.537A pdb=" N GLN F 246 " --> pdb=" O HIS F 242 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 272 removed outlier: 4.155A pdb=" N LEU F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 293 removed outlier: 3.631A pdb=" N LEU F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.595A pdb=" N ASN F 309 " --> pdb=" O LEU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 329 removed outlier: 4.131A pdb=" N GLU F 328 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 340 removed outlier: 4.271A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 346 through 350 removed outlier: 3.575A pdb=" N GLU F 349 " --> pdb=" O GLN F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 383 removed outlier: 3.858A pdb=" N LYS F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE F 361 " --> pdb=" O GLN F 357 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 364 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET F 365 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 394 removed outlier: 4.062A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 406 removed outlier: 3.956A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 419 removed outlier: 4.200A pdb=" N LYS F 414 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 Processing helix chain 'F' and resid 426 through 446 removed outlier: 4.010A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG F 436 " --> pdb=" O THR F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 4.782A pdb=" N THR F 459 " --> pdb=" O HIS F 455 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS F 462 " --> pdb=" O GLU F 458 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG F 465 " --> pdb=" O ASN F 461 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 471 " --> pdb=" O SER F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 487 removed outlier: 3.574A pdb=" N LEU F 483 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET F 487 " --> pdb=" O LEU F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 497 removed outlier: 3.654A pdb=" N LYS F 496 " --> pdb=" O ASP F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 removed outlier: 3.613A pdb=" N ALA F 501 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS F 502 " --> pdb=" O LYS F 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 498 through 502' Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.574A pdb=" N PHE F 522 " --> pdb=" O LEU F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 548 removed outlier: 3.867A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F 547 " --> pdb=" O ALA F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 564 removed outlier: 3.560A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N MET F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 579 removed outlier: 3.750A pdb=" N LYS F 578 " --> pdb=" O GLU F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 597 Processing helix chain 'G' and resid 4 through 17 removed outlier: 4.310A pdb=" N ARG G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP G 9 " --> pdb=" O GLY G 5 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE G 12 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY G 16 " --> pdb=" O ILE G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 removed outlier: 3.570A pdb=" N LYS G 30 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA G 31 " --> pdb=" O ALA G 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 27 through 31' Processing helix chain 'G' and resid 34 through 47 removed outlier: 3.520A pdb=" N GLN G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP G 44 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL G 45 " --> pdb=" O MET G 41 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 69 removed outlier: 3.588A pdb=" N TYR G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA G 65 " --> pdb=" O LYS G 61 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 97 removed outlier: 3.556A pdb=" N LYS G 94 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 104 Processing helix chain 'G' and resid 149 through 153 removed outlier: 4.233A pdb=" N SER G 153 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 156 No H-bonds generated for 'chain 'G' and resid 154 through 156' Processing helix chain 'G' and resid 157 through 168 removed outlier: 4.567A pdb=" N PHE G 163 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE G 167 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 234 through 245 removed outlier: 4.142A pdb=" N GLU G 238 " --> pdb=" O THR G 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.615A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 23 through 31 current: chain 'A' and resid 199 through 207 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.864A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 55 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.712A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 18 removed outlier: 6.697A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 7.736A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.869A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.078A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 96 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.595A pdb=" N ILE C 138 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.573A pdb=" N HIS C 150 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.537A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.907A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.767A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.760A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 634 through 638 Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 752 removed outlier: 3.560A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 732 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.795A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 835 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 830 through 835 current: chain 'C' and resid 1046 through 1058 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.961A pdb=" N GLU C 849 " --> pdb=" O VAL C 887 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 887 " --> pdb=" O GLU C 849 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 350 through 357 current: chain 'D' and resid 434 through 437 Processing sheet with id=AD1, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD2, first strand: chain 'C' and resid 1338 through 1341 removed outlier: 3.682A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 103 through 111 removed outlier: 3.640A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.570A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 368 through 369 removed outlier: 6.030A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 548 through 559 removed outlier: 3.834A pdb=" N ILE D 552 " --> pdb=" O SER D 568 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 556 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP D 558 " --> pdb=" O GLU D 562 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.978A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 956 through 957 removed outlier: 3.707A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE1, first strand: chain 'D' and resid 981 through 985 Processing sheet with id=AE2, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE3, first strand: chain 'D' and resid 1028 through 1029 removed outlier: 3.874A pdb=" N ASP D1119 " --> pdb=" O THR D1029 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1034 through 1035 removed outlier: 3.820A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1176 through 1178 removed outlier: 3.588A pdb=" N GLU D1202 " --> pdb=" O VAL D1163 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1263 through 1265 Processing sheet with id=AE7, first strand: chain 'G' and resid 109 through 110 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 109 through 110 current: chain 'G' and resid 197 through 203 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 197 through 203 current: chain 'G' and resid 280 through 288 No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 185 through 186 removed outlier: 3.542A pdb=" N ARG G 185 " --> pdb=" O GLU G 195 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9509 1.33 - 1.45: 6496 1.45 - 1.57: 18935 1.57 - 1.70: 255 1.70 - 1.82: 247 Bond restraints: 35442 Sorted by residual: bond pdb=" C1' DT 1 77 " pdb=" N1 DT 1 77 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.36e+01 bond pdb=" C1' DT 2 21 " pdb=" N1 DT 2 21 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.21e+01 bond pdb=" C1' DT 2 10 " pdb=" N1 DT 2 10 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.07e+01 bond pdb=" C1' DC 2 7 " pdb=" N1 DC 2 7 " ideal model delta sigma weight residual 1.468 1.540 -0.072 1.40e-02 5.10e+03 2.62e+01 bond pdb=" C1' DT 2 24 " pdb=" N1 DT 2 24 " ideal model delta sigma weight residual 1.468 1.540 -0.072 1.40e-02 5.10e+03 2.61e+01 ... (remaining 35437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 47180 2.51 - 5.01: 1113 5.01 - 7.52: 117 7.52 - 10.03: 23 10.03 - 12.53: 1 Bond angle restraints: 48434 Sorted by residual: angle pdb=" N ILE D 124 " pdb=" CA ILE D 124 " pdb=" C ILE D 124 " ideal model delta sigma weight residual 113.53 105.26 8.27 9.80e-01 1.04e+00 7.13e+01 angle pdb=" N VAL B 192 " pdb=" CA VAL B 192 " pdb=" C VAL B 192 " ideal model delta sigma weight residual 110.05 102.01 8.04 1.09e+00 8.42e-01 5.44e+01 angle pdb=" N SER F 602 " pdb=" CA SER F 602 " pdb=" C SER F 602 " ideal model delta sigma weight residual 114.62 107.74 6.88 1.14e+00 7.69e-01 3.64e+01 angle pdb=" O4' DA 2 33 " pdb=" C4' DA 2 33 " pdb=" C3' DA 2 33 " ideal model delta sigma weight residual 106.00 102.77 3.23 6.00e-01 2.78e+00 2.89e+01 angle pdb=" O4' DT 2 14 " pdb=" C4' DT 2 14 " pdb=" C3' DT 2 14 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.83e+01 ... (remaining 48429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 20469 35.58 - 71.17: 954 71.17 - 106.75: 36 106.75 - 142.33: 2 142.33 - 177.91: 3 Dihedral angle restraints: 21464 sinusoidal: 9758 harmonic: 11706 Sorted by residual: dihedral pdb=" CA LEU D1292 " pdb=" C LEU D1292 " pdb=" N GLU D1293 " pdb=" CA GLU D1293 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA SER C 398 " pdb=" C SER C 398 " pdb=" N ALA C 399 " pdb=" CA ALA C 399 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N VAL B 192 " pdb=" CA VAL B 192 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 21461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3854 0.054 - 0.108: 1287 0.108 - 0.162: 293 0.162 - 0.216: 51 0.216 - 0.271: 11 Chirality restraints: 5496 Sorted by residual: chirality pdb=" CB ILE G 50 " pdb=" CA ILE G 50 " pdb=" CG1 ILE G 50 " pdb=" CG2 ILE G 50 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB ILE C 561 " pdb=" CA ILE C 561 " pdb=" CG1 ILE C 561 " pdb=" CG2 ILE C 561 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE C 269 " pdb=" CA ILE C 269 " pdb=" CG1 ILE C 269 " pdb=" CG2 ILE C 269 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 5493 not shown) Planarity restraints: 5875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D1216 " -0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO D1217 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D1217 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D1217 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.92e+00 pdb=" N PRO C 190 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 528 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C LEU F 528 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU F 528 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU F 529 " 0.016 2.00e-02 2.50e+03 ... (remaining 5872 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 562 2.61 - 3.18: 27944 3.18 - 3.76: 54879 3.76 - 4.33: 73884 4.33 - 4.90: 115118 Nonbonded interactions: 272387 Sorted by model distance: nonbonded pdb=" OD2 ASP D 464 " pdb="MG MG D1503 " model vdw 2.039 2.170 nonbonded pdb=" O ASP D 460 " pdb="MG MG D1503 " model vdw 2.082 2.170 nonbonded pdb=" N ASP D 460 " pdb="MG MG D1503 " model vdw 2.099 2.250 nonbonded pdb=" O4 DT 2 44 " pdb=" O6 DG 2 45 " model vdw 2.124 3.040 nonbonded pdb=" N6 DA 1 36 " pdb=" C2 DA 1 37 " model vdw 2.220 3.420 ... (remaining 272382 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 group one per residue 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 38.270 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 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 : 0.007 0.309 35449 Z= 0.375 Angle : 1.000 54.929 48440 Z= 0.587 Chirality : 0.057 0.271 5496 Planarity : 0.007 0.088 5875 Dihedral : 18.491 177.914 13918 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.88 % Favored : 91.95 % Rotamer: Outliers : 0.86 % Allowed : 10.86 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: -4.94 (0.10), residues: 4037 helix: -4.44 (0.06), residues: 1300 sheet: -2.19 (0.24), residues: 390 loop : -2.85 (0.11), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 371 TYR 0.036 0.002 TYR F 148 PHE 0.032 0.002 PHE D1325 TRP 0.023 0.002 TRP D 580 HIS 0.007 0.002 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.36 (35442) covalent geometry : angle 0.95718 / 0.58 (48434) hydrogen bonds : bond 0.31872 / 21.33 ( 899) hydrogen bonds : angle 11.00452 / 7.60 ( 2422) metal coordination : bond 0.20496 / 10.04 ( 7) metal coordination : angle 26.03161 / 16.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.4984 (tm-30) cc_final: 0.4541 (pm20) REVERT: C 124 MET cc_start: 0.8512 (pmm) cc_final: 0.7411 (pmm) REVERT: C 130 MET cc_start: 0.8632 (ttm) cc_final: 0.8336 (tpp) REVERT: C 239 MET cc_start: 0.4903 (ptt) cc_final: 0.4641 (ptt) REVERT: C 279 LYS cc_start: 0.8071 (tptm) cc_final: 0.7802 (tppt) REVERT: C 653 MET cc_start: 0.7713 (ttp) cc_final: 0.7080 (ttp) REVERT: C 768 MET cc_start: 0.7647 (tmm) cc_final: 0.7415 (tmm) REVERT: C 796 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7446 (pp) REVERT: C 1085 MET cc_start: 0.8542 (mmm) cc_final: 0.8331 (mmm) REVERT: C 1315 MET cc_start: 0.7187 (ttt) cc_final: 0.5718 (ppp) REVERT: D 102 MET cc_start: 0.7582 (mtp) cc_final: 0.7326 (ttm) REVERT: D 114 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.6927 (mp) REVERT: D 130 MET cc_start: 0.7824 (mtm) cc_final: 0.7614 (mmm) REVERT: D 400 MET cc_start: 0.7920 (mtp) cc_final: 0.7489 (ttp) REVERT: D 484 MET cc_start: 0.8029 (mtm) cc_final: 0.7075 (ptp) REVERT: D 953 LYS cc_start: 0.5486 (mmpt) cc_final: 0.5073 (ptmm) REVERT: E 30 MET cc_start: 0.7244 (mtp) cc_final: 0.6508 (mmm) REVERT: E 61 ASN cc_start: 0.5764 (t0) cc_final: 0.5231 (p0) REVERT: F 102 MET cc_start: 0.7128 (mtp) cc_final: 0.6372 (ttp) REVERT: F 111 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6209 (mm) REVERT: F 228 TYR cc_start: 0.6162 (t80) cc_final: 0.5930 (t80) REVERT: F 456 MET cc_start: 0.7801 (mpp) cc_final: 0.7553 (mpp) REVERT: F 584 ARG cc_start: 0.6809 (ptt-90) cc_final: 0.5799 (mtp180) REVERT: G 41 MET cc_start: 0.8007 (ttm) cc_final: 0.7563 (ptp) outliers start: 30 outliers final: 14 residues processed: 236 average time/residue: 0.2336 time to fit residues: 89.0015 Evaluate side-chains 161 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN B 23 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS C 447 HIS C 513 GLN C 628 HIS C 658 GLN C 659 GLN C 760 ASN C 762 ASN C 799 ASN C 922 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1175 ASN C1220 GLN C1237 HIS C1324 ASN D 276 ASN D 419 HIS D 469 HIS D 560 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 HIS D1049 GLN D1126 GLN ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 HIS ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN G 220 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.051918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.041569 restraints weight = 328077.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.040827 restraints weight = 272954.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.041023 restraints weight = 231760.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.041080 restraints weight = 198419.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.041125 restraints weight = 177266.998| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 35449 Z= 0.168 Angle : 0.715 19.391 48440 Z= 0.381 Chirality : 0.047 0.379 5496 Planarity : 0.006 0.071 5875 Dihedral : 18.333 175.913 5886 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.94 % Favored : 93.01 % Rotamer: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.14 (0.11), residues: 4037 helix: -3.37 (0.10), residues: 1384 sheet: -1.85 (0.25), residues: 370 loop : -2.53 (0.11), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1123 TYR 0.044 0.002 TYR F 148 PHE 0.020 0.002 PHE F 266 TRP 0.017 0.001 TRP D 409 HIS 0.008 0.001 HIS C 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (35442) covalent geometry : angle 0.70554 / 0.38 (48434) hydrogen bonds : bond 0.06966 / 4.74 ( 899) hydrogen bonds : angle 6.73912 / 4.64 ( 2422) metal coordination : bond 0.01286 / 0.65 ( 7) metal coordination : angle 10.34089 / 5.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.4983 (tm-30) cc_final: 0.4516 (pm20) REVERT: B 205 MET cc_start: 0.6281 (tmm) cc_final: 0.6040 (tmm) REVERT: C 124 MET cc_start: 0.8084 (pmm) cc_final: 0.7554 (pmm) REVERT: C 130 MET cc_start: 0.8697 (ttm) cc_final: 0.8359 (tpp) REVERT: C 286 GLU cc_start: 0.7124 (pm20) cc_final: 0.6645 (pp20) REVERT: C 653 MET cc_start: 0.7937 (ttp) cc_final: 0.7454 (ttp) REVERT: C 768 MET cc_start: 0.7795 (tmm) cc_final: 0.7543 (tmm) REVERT: C 1066 MET cc_start: 0.8362 (tpt) cc_final: 0.7972 (mmm) REVERT: C 1107 MET cc_start: 0.7574 (mtm) cc_final: 0.7285 (mtm) REVERT: D 102 MET cc_start: 0.7799 (mtp) cc_final: 0.7297 (ttm) REVERT: D 130 MET cc_start: 0.7803 (mtm) cc_final: 0.7465 (mmm) REVERT: D 484 MET cc_start: 0.8582 (mtm) cc_final: 0.6879 (ptp) REVERT: D 513 MET cc_start: 0.8422 (ttt) cc_final: 0.7624 (tpt) REVERT: D 697 MET cc_start: 0.7338 (ptp) cc_final: 0.7134 (ptp) REVERT: D 698 MET cc_start: 0.6243 (mmt) cc_final: 0.5820 (mmm) REVERT: D 747 MET cc_start: 0.6650 (mmm) cc_final: 0.6284 (mmm) REVERT: D 953 LYS cc_start: 0.5368 (mmpt) cc_final: 0.4939 (ptmm) REVERT: E 30 MET cc_start: 0.7577 (mtp) cc_final: 0.7214 (mmm) REVERT: F 413 MET cc_start: 0.8682 (ptp) cc_final: 0.8465 (ptp) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.2031 time to fit residues: 59.0727 Evaluate side-chains 135 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 55 optimal weight: 0.0010 chunk 163 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 381 optimal weight: 50.0000 chunk 105 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 overall best weight: 7.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS D 469 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 GLN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN G 204 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.051621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.041443 restraints weight = 331217.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.040668 restraints weight = 269571.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.040798 restraints weight = 241634.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.040934 restraints weight = 208111.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.040953 restraints weight = 181062.289| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35449 Z= 0.194 Angle : 0.697 13.342 48440 Z= 0.370 Chirality : 0.047 0.331 5496 Planarity : 0.006 0.071 5875 Dihedral : 18.309 173.683 5886 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.27 % Favored : 91.70 % Rotamer: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.73 (0.11), residues: 4037 helix: -2.81 (0.11), residues: 1402 sheet: -1.84 (0.25), residues: 399 loop : -2.39 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 272 TYR 0.036 0.002 TYR F 148 PHE 0.020 0.002 PHE C 136 TRP 0.017 0.002 TRP D 409 HIS 0.011 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (35442) covalent geometry : angle 0.69208 / 0.37 (48434) hydrogen bonds : bond 0.06258 / 4.22 ( 899) hydrogen bonds : angle 6.24368 / 4.29 ( 2422) metal coordination : bond 0.01304 / 0.60 ( 7) metal coordination : angle 7.81073 / 4.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8114 (mtp) cc_final: 0.7706 (mtp) REVERT: B 165 GLU cc_start: 0.4384 (tm-30) cc_final: 0.4034 (pm20) REVERT: B 205 MET cc_start: 0.6307 (tmm) cc_final: 0.6071 (tmm) REVERT: C 124 MET cc_start: 0.8234 (pmm) cc_final: 0.7480 (pmm) REVERT: C 130 MET cc_start: 0.8731 (ttm) cc_final: 0.8338 (tpp) REVERT: C 653 MET cc_start: 0.7807 (ttp) cc_final: 0.7134 (ttp) REVERT: C 768 MET cc_start: 0.7966 (tmm) cc_final: 0.7658 (tmm) REVERT: D 102 MET cc_start: 0.7742 (mtp) cc_final: 0.7316 (ttm) REVERT: D 130 MET cc_start: 0.7771 (mtm) cc_final: 0.7562 (mtp) REVERT: D 484 MET cc_start: 0.8634 (mtm) cc_final: 0.7022 (ptp) REVERT: D 513 MET cc_start: 0.8489 (ttt) cc_final: 0.7699 (tpt) REVERT: D 644 MET cc_start: 0.6973 (tpt) cc_final: 0.6550 (tpp) REVERT: D 697 MET cc_start: 0.7178 (ptp) cc_final: 0.6956 (ptp) REVERT: D 698 MET cc_start: 0.6556 (mmt) cc_final: 0.6142 (mmm) REVERT: D 953 LYS cc_start: 0.5360 (mmpt) cc_final: 0.4857 (ptmm) REVERT: E 30 MET cc_start: 0.7563 (mtp) cc_final: 0.7135 (mmm) REVERT: F 297 MET cc_start: 0.3892 (mtm) cc_final: 0.2813 (mmm) REVERT: F 365 MET cc_start: 0.8189 (tmm) cc_final: 0.7817 (ptt) REVERT: F 413 MET cc_start: 0.8679 (ptp) cc_final: 0.8470 (ptp) REVERT: F 456 MET cc_start: 0.8448 (mpp) cc_final: 0.8100 (mpp) outliers start: 1 outliers final: 1 residues processed: 171 average time/residue: 0.2091 time to fit residues: 60.6251 Evaluate side-chains 134 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 219 optimal weight: 10.0000 chunk 82 optimal weight: 0.0370 chunk 335 optimal weight: 9.9990 chunk 368 optimal weight: 30.0000 chunk 322 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 378 optimal weight: 50.0000 chunk 112 optimal weight: 0.0470 chunk 75 optimal weight: 20.0000 chunk 282 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 overall best weight: 3.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN D 469 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN G 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.051977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.041896 restraints weight = 330421.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.041146 restraints weight = 265995.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.041297 restraints weight = 239980.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041371 restraints weight = 208712.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.041392 restraints weight = 186278.359| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35449 Z= 0.129 Angle : 0.626 11.865 48440 Z= 0.334 Chirality : 0.045 0.345 5496 Planarity : 0.005 0.085 5875 Dihedral : 18.232 173.340 5886 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.32 (0.12), residues: 4037 helix: -2.35 (0.12), residues: 1393 sheet: -1.67 (0.25), residues: 389 loop : -2.22 (0.12), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 40 TYR 0.025 0.001 TYR F 148 PHE 0.016 0.001 PHE D 620 TRP 0.016 0.001 TRP D 409 HIS 0.005 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (35442) covalent geometry : angle 0.62162 / 0.33 (48434) hydrogen bonds : bond 0.05220 / 3.54 ( 899) hydrogen bonds : angle 5.80082 / 3.99 ( 2422) metal coordination : bond 0.00620 / 0.29 ( 7) metal coordination : angle 6.81471 / 3.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.4538 (tm-30) cc_final: 0.4225 (pm20) REVERT: B 205 MET cc_start: 0.6551 (tmm) cc_final: 0.6125 (tmm) REVERT: C 124 MET cc_start: 0.8210 (pmm) cc_final: 0.7532 (pmm) REVERT: C 459 MET cc_start: 0.7713 (mtm) cc_final: 0.7512 (mtt) REVERT: C 653 MET cc_start: 0.7738 (ttp) cc_final: 0.7022 (ttp) REVERT: C 768 MET cc_start: 0.7925 (tmm) cc_final: 0.7640 (tmm) REVERT: C 1085 MET cc_start: 0.8453 (mmt) cc_final: 0.8249 (mmt) REVERT: C 1107 MET cc_start: 0.7571 (mtm) cc_final: 0.7229 (mtm) REVERT: D 102 MET cc_start: 0.7761 (mtp) cc_final: 0.7318 (ttm) REVERT: D 130 MET cc_start: 0.7759 (mtm) cc_final: 0.7503 (mmm) REVERT: D 484 MET cc_start: 0.8465 (mtm) cc_final: 0.6863 (ptp) REVERT: D 513 MET cc_start: 0.8169 (ttt) cc_final: 0.7501 (tpt) REVERT: D 644 MET cc_start: 0.7069 (tpt) cc_final: 0.6835 (tpp) REVERT: D 698 MET cc_start: 0.6520 (mmt) cc_final: 0.6120 (mmm) REVERT: D 953 LYS cc_start: 0.5350 (mmpt) cc_final: 0.5133 (pptt) REVERT: E 30 MET cc_start: 0.7510 (mtp) cc_final: 0.7154 (mmm) REVERT: F 365 MET cc_start: 0.8171 (tmm) cc_final: 0.7720 (ptt) REVERT: F 413 MET cc_start: 0.8658 (ptp) cc_final: 0.8423 (ptp) REVERT: F 456 MET cc_start: 0.8366 (mpp) cc_final: 0.8046 (mpp) REVERT: G 13 TRP cc_start: 0.6515 (t60) cc_final: 0.6275 (t60) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2029 time to fit residues: 59.8139 Evaluate side-chains 137 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 179 optimal weight: 20.0000 chunk 176 optimal weight: 0.0060 chunk 3 optimal weight: 20.0000 chunk 362 optimal weight: 8.9990 chunk 275 optimal weight: 7.9990 chunk 11 optimal weight: 30.0000 chunk 296 optimal weight: 0.0000 chunk 121 optimal weight: 0.1980 chunk 293 optimal weight: 0.1980 chunk 338 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN F 362 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.052392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041757 restraints weight = 328745.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.041165 restraints weight = 261224.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.041395 restraints weight = 214079.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041423 restraints weight = 195894.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.041475 restraints weight = 170805.282| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35449 Z= 0.114 Angle : 0.595 14.138 48440 Z= 0.317 Chirality : 0.044 0.352 5496 Planarity : 0.004 0.075 5875 Dihedral : 18.095 175.487 5886 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.00 (0.12), residues: 4037 helix: -1.99 (0.12), residues: 1409 sheet: -1.46 (0.25), residues: 394 loop : -2.10 (0.12), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 40 TYR 0.028 0.001 TYR F 148 PHE 0.019 0.001 PHE F 266 TRP 0.013 0.001 TRP D 409 HIS 0.005 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (35442) covalent geometry : angle 0.58957 / 0.32 (48434) hydrogen bonds : bond 0.04616 / 3.15 ( 899) hydrogen bonds : angle 5.36113 / 3.69 ( 2422) metal coordination : bond 0.00952 / 0.53 ( 7) metal coordination : angle 7.15974 / 3.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.4635 (tm-30) cc_final: 0.4272 (pm20) REVERT: C 124 MET cc_start: 0.8181 (pmm) cc_final: 0.7550 (pmm) REVERT: C 275 ARG cc_start: 0.7469 (mpp-170) cc_final: 0.7260 (mpp80) REVERT: C 653 MET cc_start: 0.7877 (ttp) cc_final: 0.7417 (ttp) REVERT: C 768 MET cc_start: 0.7935 (tmm) cc_final: 0.7619 (tmm) REVERT: D 102 MET cc_start: 0.7780 (mtp) cc_final: 0.7392 (ttm) REVERT: D 130 MET cc_start: 0.7766 (mtm) cc_final: 0.7508 (mmm) REVERT: D 400 MET cc_start: 0.7931 (mtm) cc_final: 0.7503 (mtm) REVERT: D 484 MET cc_start: 0.8473 (mtm) cc_final: 0.8224 (mtp) REVERT: D 513 MET cc_start: 0.8229 (ttt) cc_final: 0.7231 (tpt) REVERT: D 644 MET cc_start: 0.7272 (tpt) cc_final: 0.6956 (tpp) REVERT: D 698 MET cc_start: 0.6258 (mmt) cc_final: 0.5817 (mmm) REVERT: D 953 LYS cc_start: 0.5240 (mmpt) cc_final: 0.4983 (pptt) REVERT: E 30 MET cc_start: 0.7454 (mtp) cc_final: 0.7072 (mmm) REVERT: F 102 MET cc_start: 0.6420 (ttp) cc_final: 0.6162 (ttp) REVERT: F 365 MET cc_start: 0.8325 (tmm) cc_final: 0.7691 (ptt) REVERT: F 413 MET cc_start: 0.8663 (ptp) cc_final: 0.8397 (ptp) REVERT: F 456 MET cc_start: 0.8386 (mpp) cc_final: 0.8125 (mpp) REVERT: F 474 MET cc_start: 0.6464 (mtp) cc_final: 0.4833 (mmp) REVERT: G 159 MET cc_start: 0.2736 (mtt) cc_final: 0.1843 (tpt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1946 time to fit residues: 58.3537 Evaluate side-chains 139 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 196 optimal weight: 9.9990 chunk 337 optimal weight: 2.9990 chunk 259 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 301 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 chunk 234 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN G 194 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.052027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.041155 restraints weight = 329607.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.040540 restraints weight = 264243.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040658 restraints weight = 223581.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040789 restraints weight = 190205.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040828 restraints weight = 166453.947| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35449 Z= 0.155 Angle : 0.631 13.269 48440 Z= 0.333 Chirality : 0.045 0.360 5496 Planarity : 0.005 0.071 5875 Dihedral : 18.099 176.669 5886 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.82 (0.12), residues: 4037 helix: -1.75 (0.13), residues: 1412 sheet: -1.39 (0.26), residues: 390 loop : -2.06 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 143 TYR 0.021 0.002 TYR F 148 PHE 0.017 0.002 PHE D1325 TRP 0.014 0.001 TRP D 409 HIS 0.006 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (35442) covalent geometry : angle 0.62625 / 0.33 (48434) hydrogen bonds : bond 0.04709 / 3.21 ( 899) hydrogen bonds : angle 5.34802 / 3.67 ( 2422) metal coordination : bond 0.01007 / 0.45 ( 7) metal coordination : angle 6.64148 / 3.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.4236 (tm-30) cc_final: 0.3927 (pm20) REVERT: C 124 MET cc_start: 0.8272 (pmm) cc_final: 0.7490 (pmm) REVERT: C 239 MET cc_start: 0.5276 (ptt) cc_final: 0.4820 (mmm) REVERT: C 653 MET cc_start: 0.8058 (ttp) cc_final: 0.7356 (ttp) REVERT: C 1085 MET cc_start: 0.8388 (mmt) cc_final: 0.7882 (ttm) REVERT: C 1107 MET cc_start: 0.7823 (mtm) cc_final: 0.7553 (mtm) REVERT: C 1319 MET cc_start: 0.7848 (ttp) cc_final: 0.7632 (ttp) REVERT: D 102 MET cc_start: 0.7760 (mtp) cc_final: 0.7271 (ttm) REVERT: D 130 MET cc_start: 0.7844 (mtm) cc_final: 0.7485 (mtp) REVERT: D 400 MET cc_start: 0.8503 (mtm) cc_final: 0.8045 (ttm) REVERT: D 484 MET cc_start: 0.8869 (mtm) cc_final: 0.7162 (ptp) REVERT: D 513 MET cc_start: 0.8625 (ttt) cc_final: 0.7578 (tpt) REVERT: D 644 MET cc_start: 0.7402 (tpt) cc_final: 0.7186 (tpp) REVERT: D 698 MET cc_start: 0.6713 (mmt) cc_final: 0.6030 (mmt) REVERT: D 953 LYS cc_start: 0.5175 (mmpt) cc_final: 0.4927 (pptt) REVERT: E 30 MET cc_start: 0.7462 (mtp) cc_final: 0.6967 (mmm) REVERT: F 100 MET cc_start: 0.8209 (mtt) cc_final: 0.7816 (mtt) REVERT: F 102 MET cc_start: 0.6626 (ttp) cc_final: 0.6401 (ttp) REVERT: F 365 MET cc_start: 0.8401 (tmm) cc_final: 0.7653 (ptt) REVERT: F 413 MET cc_start: 0.8787 (ptp) cc_final: 0.8502 (ptp) REVERT: F 456 MET cc_start: 0.8578 (mpp) cc_final: 0.8295 (mpp) REVERT: F 474 MET cc_start: 0.6945 (mtp) cc_final: 0.4858 (mmp) outliers start: 1 outliers final: 1 residues processed: 166 average time/residue: 0.2008 time to fit residues: 57.4618 Evaluate side-chains 137 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 333 optimal weight: 6.9990 chunk 115 optimal weight: 30.0000 chunk 247 optimal weight: 4.9990 chunk 316 optimal weight: 6.9990 chunk 217 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 chunk 262 optimal weight: 20.0000 chunk 328 optimal weight: 30.0000 chunk 315 optimal weight: 0.0170 chunk 342 optimal weight: 10.0000 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN G 37 HIS ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.052089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.041537 restraints weight = 333035.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040965 restraints weight = 267711.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.040975 restraints weight = 215446.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.041087 restraints weight = 199372.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.041105 restraints weight = 180405.053| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35449 Z= 0.140 Angle : 0.611 11.839 48440 Z= 0.323 Chirality : 0.045 0.365 5496 Planarity : 0.004 0.068 5875 Dihedral : 18.062 176.843 5886 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.13 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.65 (0.12), residues: 4037 helix: -1.56 (0.13), residues: 1414 sheet: -1.27 (0.26), residues: 380 loop : -2.00 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 40 TYR 0.021 0.001 TYR F 148 PHE 0.019 0.001 PHE D 620 TRP 0.013 0.001 TRP D 409 HIS 0.006 0.001 HIS G 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (35442) covalent geometry : angle 0.60700 / 0.32 (48434) hydrogen bonds : bond 0.04467 / 3.06 ( 899) hydrogen bonds : angle 5.27457 / 3.62 ( 2422) metal coordination : bond 0.01085 / 0.47 ( 7) metal coordination : angle 6.08058 / 3.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 GLU cc_start: 0.4250 (tm-30) cc_final: 0.3931 (pm20) REVERT: C 124 MET cc_start: 0.8295 (pmm) cc_final: 0.7475 (pmm) REVERT: C 239 MET cc_start: 0.5429 (ptt) cc_final: 0.4887 (mmm) REVERT: C 429 MET cc_start: 0.8751 (mtm) cc_final: 0.7661 (mtp) REVERT: C 515 MET cc_start: 0.6724 (tmm) cc_final: 0.6251 (tmm) REVERT: C 653 MET cc_start: 0.7948 (ttp) cc_final: 0.7203 (ttp) REVERT: C 1085 MET cc_start: 0.8416 (mmt) cc_final: 0.8205 (mmt) REVERT: C 1107 MET cc_start: 0.7850 (mtm) cc_final: 0.7555 (mtm) REVERT: D 102 MET cc_start: 0.7738 (mtp) cc_final: 0.7281 (ttm) REVERT: D 130 MET cc_start: 0.7844 (mtm) cc_final: 0.7485 (mtp) REVERT: D 180 MET cc_start: 0.7198 (tpp) cc_final: 0.6219 (tpp) REVERT: D 400 MET cc_start: 0.8487 (mtm) cc_final: 0.7896 (ttm) REVERT: D 484 MET cc_start: 0.8800 (mtm) cc_final: 0.7001 (ptp) REVERT: D 513 MET cc_start: 0.8403 (ttt) cc_final: 0.7602 (tpt) REVERT: D 698 MET cc_start: 0.6580 (mmt) cc_final: 0.6330 (mmt) REVERT: D 747 MET cc_start: 0.6656 (mmp) cc_final: 0.6377 (mmp) REVERT: D 953 LYS cc_start: 0.5236 (mmpt) cc_final: 0.4931 (pptt) REVERT: F 100 MET cc_start: 0.8221 (mtt) cc_final: 0.7930 (mtt) REVERT: F 102 MET cc_start: 0.6706 (ttp) cc_final: 0.6441 (ttp) REVERT: F 365 MET cc_start: 0.8401 (tmm) cc_final: 0.8135 (tmm) REVERT: F 413 MET cc_start: 0.8773 (ptp) cc_final: 0.8481 (ptp) REVERT: F 456 MET cc_start: 0.8145 (mpp) cc_final: 0.7885 (mpp) REVERT: F 474 MET cc_start: 0.7140 (mtp) cc_final: 0.5041 (mmp) REVERT: F 507 MET cc_start: 0.8281 (ptm) cc_final: 0.7772 (ppp) REVERT: G 159 MET cc_start: 0.2839 (mtt) cc_final: 0.1883 (tpt) REVERT: G 198 TYR cc_start: 0.4655 (t80) cc_final: 0.4352 (t80) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2069 time to fit residues: 58.1444 Evaluate side-chains 137 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 82 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 365 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 400 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 280 optimal weight: 20.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN G 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.051889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.041077 restraints weight = 332888.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.040582 restraints weight = 265875.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.040717 restraints weight = 226778.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.040773 restraints weight = 212670.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.040845 restraints weight = 180691.809| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35449 Z= 0.161 Angle : 0.629 11.291 48440 Z= 0.332 Chirality : 0.045 0.366 5496 Planarity : 0.005 0.068 5875 Dihedral : 18.071 177.337 5886 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.68 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.58 (0.13), residues: 4037 helix: -1.49 (0.13), residues: 1408 sheet: -1.23 (0.26), residues: 374 loop : -1.96 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 274 TYR 0.023 0.001 TYR F 148 PHE 0.017 0.001 PHE C 405 TRP 0.013 0.001 TRP D 409 HIS 0.006 0.001 HIS D1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (35442) covalent geometry : angle 0.62498 / 0.33 (48434) hydrogen bonds : bond 0.04576 / 3.13 ( 899) hydrogen bonds : angle 5.28752 / 3.62 ( 2422) metal coordination : bond 0.00857 / 0.38 ( 7) metal coordination : angle 6.34840 / 3.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 MET cc_start: 0.8347 (pmm) cc_final: 0.7476 (pmm) REVERT: C 239 MET cc_start: 0.5482 (ptt) cc_final: 0.4866 (mmm) REVERT: C 515 MET cc_start: 0.6691 (tmm) cc_final: 0.6241 (tmm) REVERT: C 653 MET cc_start: 0.7827 (ttp) cc_final: 0.7159 (ttp) REVERT: C 1107 MET cc_start: 0.7826 (mtm) cc_final: 0.7513 (mtm) REVERT: D 130 MET cc_start: 0.7825 (mtm) cc_final: 0.7468 (mtp) REVERT: D 180 MET cc_start: 0.7355 (tpp) cc_final: 0.6401 (tpp) REVERT: D 400 MET cc_start: 0.8642 (mtm) cc_final: 0.8070 (ttm) REVERT: D 484 MET cc_start: 0.8858 (mtm) cc_final: 0.8524 (mtp) REVERT: D 513 MET cc_start: 0.8505 (ttt) cc_final: 0.7792 (tpt) REVERT: D 747 MET cc_start: 0.6670 (mmp) cc_final: 0.6393 (mmp) REVERT: D 953 LYS cc_start: 0.5201 (mmpt) cc_final: 0.4810 (ptmm) REVERT: F 100 MET cc_start: 0.8178 (mtt) cc_final: 0.7846 (mtt) REVERT: F 102 MET cc_start: 0.6733 (ttp) cc_final: 0.6450 (ttp) REVERT: F 413 MET cc_start: 0.8777 (ptp) cc_final: 0.8481 (ptp) REVERT: F 456 MET cc_start: 0.8116 (mpp) cc_final: 0.7832 (mpp) REVERT: F 507 MET cc_start: 0.8200 (ptm) cc_final: 0.7635 (ppp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2008 time to fit residues: 55.9989 Evaluate side-chains 138 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 288 optimal weight: 7.9990 chunk 383 optimal weight: 50.0000 chunk 343 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 chunk 308 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 400 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 chunk 380 optimal weight: 50.0000 chunk 295 optimal weight: 4.9990 chunk 277 optimal weight: 6.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.052116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.041648 restraints weight = 331735.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041014 restraints weight = 269012.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.041144 restraints weight = 231386.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.041257 restraints weight = 199315.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041304 restraints weight = 174057.625| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35449 Z= 0.123 Angle : 0.599 11.694 48440 Z= 0.316 Chirality : 0.044 0.371 5496 Planarity : 0.004 0.066 5875 Dihedral : 18.023 177.495 5886 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.94 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.47 (0.13), residues: 4037 helix: -1.40 (0.13), residues: 1422 sheet: -1.21 (0.26), residues: 382 loop : -1.89 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 425 TYR 0.017 0.001 TYR F 148 PHE 0.019 0.001 PHE C 405 TRP 0.014 0.001 TRP D 580 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (35442) covalent geometry : angle 0.59531 / 0.32 (48434) hydrogen bonds : bond 0.04294 / 2.94 ( 899) hydrogen bonds : angle 5.14783 / 3.53 ( 2422) metal coordination : bond 0.00689 / 0.31 ( 7) metal coordination : angle 6.06407 / 3.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8090 (mtp) cc_final: 0.7487 (mmm) REVERT: C 124 MET cc_start: 0.8347 (pmm) cc_final: 0.7475 (pmm) REVERT: C 429 MET cc_start: 0.8694 (mtm) cc_final: 0.7643 (mtp) REVERT: C 515 MET cc_start: 0.6893 (tmm) cc_final: 0.6471 (tmm) REVERT: C 653 MET cc_start: 0.7762 (ttp) cc_final: 0.7097 (ttp) REVERT: C 1085 MET cc_start: 0.8245 (mmt) cc_final: 0.7425 (ttm) REVERT: C 1107 MET cc_start: 0.7862 (mtm) cc_final: 0.7586 (mtm) REVERT: C 1319 MET cc_start: 0.8029 (ttp) cc_final: 0.7828 (ttp) REVERT: D 130 MET cc_start: 0.7817 (mtm) cc_final: 0.7467 (mtp) REVERT: D 180 MET cc_start: 0.7444 (tpp) cc_final: 0.6466 (tpp) REVERT: D 400 MET cc_start: 0.8589 (mtm) cc_final: 0.8016 (ttm) REVERT: D 484 MET cc_start: 0.8794 (mtm) cc_final: 0.8555 (mtm) REVERT: D 513 MET cc_start: 0.8438 (ttt) cc_final: 0.7449 (tpt) REVERT: D 747 MET cc_start: 0.6605 (mmp) cc_final: 0.6349 (mmp) REVERT: D 953 LYS cc_start: 0.5301 (mmpt) cc_final: 0.4866 (ptmm) REVERT: E 6 VAL cc_start: 0.7049 (m) cc_final: 0.6829 (p) REVERT: F 100 MET cc_start: 0.8210 (mtt) cc_final: 0.7895 (mtt) REVERT: F 102 MET cc_start: 0.6686 (ttp) cc_final: 0.6411 (ttp) REVERT: F 413 MET cc_start: 0.8661 (ptp) cc_final: 0.8337 (ptp) REVERT: F 456 MET cc_start: 0.8056 (mpp) cc_final: 0.7793 (mpp) REVERT: F 474 MET cc_start: 0.7005 (mtp) cc_final: 0.4762 (mmp) REVERT: F 507 MET cc_start: 0.8239 (ptm) cc_final: 0.7795 (ppp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2013 time to fit residues: 56.8362 Evaluate side-chains 139 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 11 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 302 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 194 optimal weight: 0.3980 chunk 404 optimal weight: 9.9990 chunk 382 optimal weight: 50.0000 chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN G 194 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.051735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.041234 restraints weight = 330716.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.040561 restraints weight = 268986.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040791 restraints weight = 236762.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.040872 restraints weight = 208510.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040895 restraints weight = 177573.449| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35449 Z= 0.170 Angle : 0.644 10.986 48440 Z= 0.338 Chirality : 0.046 0.371 5496 Planarity : 0.005 0.067 5875 Dihedral : 18.082 177.895 5886 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.32 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.49 (0.13), residues: 4037 helix: -1.42 (0.13), residues: 1424 sheet: -1.18 (0.26), residues: 382 loop : -1.91 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 104 TYR 0.016 0.002 TYR F 148 PHE 0.019 0.002 PHE C 828 TRP 0.019 0.002 TRP G 13 HIS 0.008 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (35442) covalent geometry : angle 0.64117 / 0.34 (48434) hydrogen bonds : bond 0.04535 / 3.11 ( 899) hydrogen bonds : angle 5.26884 / 3.61 ( 2422) metal coordination : bond 0.01002 / 0.45 ( 7) metal coordination : angle 5.89035 / 3.02 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8074 Ramachandran restraints generated. 4037 Oldfield, 0 Emsley, 4037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.7798 (mtp) cc_final: 0.7361 (mmm) REVERT: C 124 MET cc_start: 0.8395 (pmm) cc_final: 0.7514 (pmm) REVERT: C 429 MET cc_start: 0.8761 (mtm) cc_final: 0.7885 (mtp) REVERT: C 515 MET cc_start: 0.6813 (tmm) cc_final: 0.6362 (tmm) REVERT: C 653 MET cc_start: 0.7647 (ttp) cc_final: 0.7018 (ttp) REVERT: C 1085 MET cc_start: 0.8100 (mmt) cc_final: 0.7265 (ttm) REVERT: C 1107 MET cc_start: 0.7650 (mtm) cc_final: 0.7333 (mtm) REVERT: C 1319 MET cc_start: 0.8101 (ttp) cc_final: 0.7609 (mtp) REVERT: D 130 MET cc_start: 0.7823 (mtm) cc_final: 0.7457 (mtp) REVERT: D 180 MET cc_start: 0.7416 (tpp) cc_final: 0.6463 (tpp) REVERT: D 400 MET cc_start: 0.8657 (mtm) cc_final: 0.8013 (ttm) REVERT: D 484 MET cc_start: 0.8853 (mtm) cc_final: 0.8648 (mtm) REVERT: D 747 MET cc_start: 0.6690 (mmp) cc_final: 0.6420 (mmp) REVERT: D 953 LYS cc_start: 0.5372 (mmpt) cc_final: 0.5005 (ptmm) REVERT: E 6 VAL cc_start: 0.7084 (m) cc_final: 0.6873 (p) REVERT: F 100 MET cc_start: 0.8167 (mtt) cc_final: 0.7823 (mtt) REVERT: F 102 MET cc_start: 0.6711 (ttp) cc_final: 0.6450 (ttp) REVERT: F 413 MET cc_start: 0.8699 (ptp) cc_final: 0.8388 (ptp) REVERT: F 456 MET cc_start: 0.8064 (mpp) cc_final: 0.7793 (mpp) REVERT: F 474 MET cc_start: 0.7185 (mtp) cc_final: 0.5102 (mmp) REVERT: F 507 MET cc_start: 0.8239 (ptm) cc_final: 0.7741 (ppp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2057 time to fit residues: 55.8095 Evaluate side-chains 138 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 104 optimal weight: 9.9990 chunk 28 optimal weight: 40.0000 chunk 385 optimal weight: 50.0000 chunk 373 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 384 optimal weight: 50.0000 chunk 313 optimal weight: 0.0010 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS D 519 ASN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN G 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.052001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.041532 restraints weight = 330999.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.040669 restraints weight = 270487.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040935 restraints weight = 228236.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.041029 restraints weight = 194548.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.041041 restraints weight = 172359.785| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35449 Z= 0.126 Angle : 0.602 11.098 48440 Z= 0.317 Chirality : 0.044 0.376 5496 Planarity : 0.004 0.066 5875 Dihedral : 18.033 177.998 5886 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.21 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.36 (0.13), residues: 4037 helix: -1.28 (0.13), residues: 1418 sheet: -1.12 (0.26), residues: 387 loop : -1.85 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 104 TYR 0.017 0.001 TYR F 148 PHE 0.018 0.001 PHE C 828 TRP 0.015 0.001 TRP D 580 HIS 0.010 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (35442) covalent geometry : angle 0.59856 / 0.32 (48434) hydrogen bonds : bond 0.04240 / 2.91 ( 899) hydrogen bonds : angle 5.11069 / 3.50 ( 2422) metal coordination : bond 0.00728 / 0.33 ( 7) metal coordination : angle 5.77620 / 2.92 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4279.72 seconds wall clock time: 75 minutes 39.44 seconds (4539.44 seconds total)