Starting phenix.real_space_refine on Sun Sep 13 11:26:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jpa_9868/09_2026/6jpa_9868.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jpa_9868/09_2026/6jpa_9868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jpa_9868/09_2026/6jpa_9868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jpa_9868/09_2026/6jpa_9868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jpa_9868/09_2026/6jpa_9868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jpa_9868/09_2026/6jpa_9868.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6jpa_9868/09_2026/6jpa_9868.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jpa_9868/09_2026/6jpa_9868.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 10 5.49 5 S 126 5.16 5 C 14414 2.51 5 N 3598 2.21 5 O 4081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s 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: 22232 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 10219 Classifications: {'peptide': 1274} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 38, 'TRANS': 1235} Chain breaks: 6 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 710 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 91} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1367 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 16, 439 Unusual residues: {' CA': 3, '3PE': 8, '4YH': 1, '9Z9': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-2': 1, '3PE:plan-1': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 16, 439 Unusual residues: {' CA': 3, '3PE': 8, '4YH': 1, '9Z9': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-2': 1, '3PE:plan-1': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 398 Chain: "F" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'ETA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.62, per 1000 atoms: 0.25 Number of scatterers: 22232 At special positions: 0 Unit cell: (168.014, 183.288, 165.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 126 16.00 P 10 15.00 O 4081 8.00 N 3598 7.00 C 14414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=1.74 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=1.88 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=1.78 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.95 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.05 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.77 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.27 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.02 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=1.57 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.02 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 Atom "HETATM22146 O5 NAG F1104 .*. O " rejected from bonding due to valence issues. Atom "HETATM22174 O5 NAG F1114 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 2 " - " NAG L 3 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG F1104 " - " ASN F 326 " " NAG F1107 " - " ASN F 891 " " NAG F1114 " - " ASN F 92 " " NAG F1115 " - " ASN F 606 " " NAG F1120 " - " ASN F 784 " " NAG F1121 " - " ASN F1001 " " NAG F1122 " - " ASN F 988 " " NAG G 1 " - " ASN F 615 " " NAG H 1 " - " ASN F 186 " " NAG I 1 " - " ASN F 470 " " NAG J 1 " - " ASN F 898 " " NAG K 1 " - " ASN F 678 " " NAG L 1 " - " ASN F 827 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.2 seconds 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 20 sheets defined 54.8% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 removed outlier: 3.732A pdb=" N GLU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.686A pdb=" N LEU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 4.259A pdb=" N ASP A 77 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.811A pdb=" N LEU A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.667A pdb=" N SER A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 144 removed outlier: 3.779A pdb=" N VAL A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 removed outlier: 3.716A pdb=" N ARG A 168 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.938A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 179' Processing helix chain 'A' and resid 179 through 193 removed outlier: 3.589A pdb=" N GLN A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 219 removed outlier: 3.560A pdb=" N LEU A 202 " --> pdb=" O HIS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.683A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 4.352A pdb=" N TYR A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 349 through 376 removed outlier: 4.011A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A 373 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 430 removed outlier: 4.042A pdb=" N HIS A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 438 through 452 removed outlier: 3.583A pdb=" N ASN A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 486 removed outlier: 3.521A pdb=" N THR A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.676A pdb=" N TYR A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 494' Processing helix chain 'A' and resid 494 through 517 removed outlier: 3.847A pdb=" N PHE A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 505 " --> pdb=" O CYS A 501 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.567A pdb=" N VAL A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 Processing helix chain 'A' and resid 542 through 559 removed outlier: 3.518A pdb=" N SER A 546 " --> pdb=" O TRP A 542 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.557A pdb=" N LEU A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 615 through 626 Processing helix chain 'A' and resid 631 through 637 removed outlier: 3.579A pdb=" N LEU A 636 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 677 removed outlier: 3.847A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.545A pdb=" N LYS A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 798 through 806 removed outlier: 4.237A pdb=" N THR A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 803 " --> pdb=" O THR A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 816 removed outlier: 3.894A pdb=" N ALA A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 832 Processing helix chain 'A' and resid 832 through 854 removed outlier: 3.665A pdb=" N PHE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 883 removed outlier: 3.515A pdb=" N LEU A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 899 removed outlier: 3.849A pdb=" N VAL A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 901 No H-bonds generated for 'chain 'A' and resid 900 through 901' Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 911 through 924 removed outlier: 3.745A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 951 Processing helix chain 'A' and resid 999 through 1012 removed outlier: 3.611A pdb=" N MET A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.715A pdb=" N LEU A1019 " --> pdb=" O GLY A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1071 removed outlier: 4.240A pdb=" N PHE A1044 " --> pdb=" O GLU A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1095 removed outlier: 3.764A pdb=" N CYS A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR A1091 " --> pdb=" O GLN A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 removed outlier: 3.564A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A1115 " --> pdb=" O VAL A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1136 removed outlier: 3.605A pdb=" N GLU A1121 " --> pdb=" O SER A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1171 removed outlier: 3.565A pdb=" N ILE A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A1151 " --> pdb=" O ASN A1147 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1206 removed outlier: 3.504A pdb=" N VAL A1184 " --> pdb=" O ASP A1180 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1238 removed outlier: 3.559A pdb=" N LEU A1237 " --> pdb=" O PHE A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1249 Processing helix chain 'A' and resid 1250 through 1262 Processing helix chain 'A' and resid 1267 through 1290 removed outlier: 4.377A pdb=" N ALA A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1321 Processing helix chain 'A' and resid 1324 through 1332 Processing helix chain 'A' and resid 1348 through 1352 removed outlier: 3.896A pdb=" N THR A1351 " --> pdb=" O GLU A1348 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS A1352 " --> pdb=" O GLU A1349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1348 through 1352' Processing helix chain 'A' and resid 1356 through 1382 Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1407 removed outlier: 3.994A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A1403 " --> pdb=" O LEU A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1427 removed outlier: 3.558A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1451 removed outlier: 4.021A pdb=" N LEU A1448 " --> pdb=" O ALA A1444 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A1449 " --> pdb=" O CYS A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1475 removed outlier: 3.673A pdb=" N LEU A1467 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A1468 " --> pdb=" O ASN A1464 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1469 " --> pdb=" O ALA A1465 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A1474 " --> pdb=" O LEU A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1493 removed outlier: 3.619A pdb=" N ALA A1486 " --> pdb=" O ASN A1482 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A1487 " --> pdb=" O PHE A1483 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A1493 " --> pdb=" O GLU A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1500 through 1506 removed outlier: 3.931A pdb=" N LYS A1504 " --> pdb=" O ARG A1500 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A1506 " --> pdb=" O SER A1502 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.947A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET E 24 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.960A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 165 removed outlier: 3.518A pdb=" N PHE E 143 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER E 154 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER E 161 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 202 removed outlier: 3.776A pdb=" N ALA E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 197 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 removed outlier: 3.598A pdb=" N ARG B 82 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 83 " --> pdb=" O MET B 79 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.991A pdb=" N ARG B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 304 removed outlier: 3.533A pdb=" N ASP C 291 " --> pdb=" O TYR C 287 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.723A pdb=" N VAL C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.567A pdb=" N SER C 378 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 removed outlier: 4.024A pdb=" N LEU C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 398 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 410 removed outlier: 3.763A pdb=" N LYS C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 410' Processing helix chain 'C' and resid 411 through 425 removed outlier: 4.043A pdb=" N GLN C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 438 through 458 removed outlier: 3.550A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 41 through 53 removed outlier: 3.800A pdb=" N GLY F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 removed outlier: 3.651A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 109 removed outlier: 3.726A pdb=" N SER F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.919A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.604A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU F 201 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 251 removed outlier: 3.863A pdb=" N GLY F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 284 removed outlier: 3.618A pdb=" N ARG F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER F 279 " --> pdb=" O ARG F 275 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'F' and resid 336 through 347 Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.826A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 408 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 433 through 438 Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.682A pdb=" N LYS F 442 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 542 through 546 removed outlier: 3.846A pdb=" N ARG F 546 " --> pdb=" O LEU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 567 removed outlier: 3.502A pdb=" N GLU F 567 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 580 Processing helix chain 'F' and resid 640 through 647 Processing helix chain 'F' and resid 652 through 656 removed outlier: 4.021A pdb=" N PHE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 693 removed outlier: 3.686A pdb=" N PHE F 689 " --> pdb=" O ASN F 685 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE F 690 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP F 691 " --> pdb=" O ASN F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 713 removed outlier: 4.022A pdb=" N ILE F 705 " --> pdb=" O ASN F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 722 removed outlier: 3.838A pdb=" N GLU F 717 " --> pdb=" O GLY F 713 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 754 removed outlier: 3.520A pdb=" N GLU F 753 " --> pdb=" O GLU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 773 removed outlier: 3.650A pdb=" N LYS F 768 " --> pdb=" O ASP F 764 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 771 " --> pdb=" O TYR F 767 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN F 773 " --> pdb=" O ARG F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 830 removed outlier: 3.507A pdb=" N GLU F 826 " --> pdb=" O ASN F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 removed outlier: 3.618A pdb=" N MET F 886 " --> pdb=" O ASP F 882 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN F 891 " --> pdb=" O ARG F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1027 Processing helix chain 'F' and resid 1045 through 1050 removed outlier: 3.753A pdb=" N MET F1049 " --> pdb=" O ASP F1045 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 957 Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA4, first strand: chain 'A' and resid 1416 through 1417 Processing sheet with id=AA5, first strand: chain 'E' and resid 48 through 50 removed outlier: 3.683A pdb=" N CYS E 57 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.457A pdb=" N ARG B 148 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE B 136 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 103 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 104 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 309 through 313 removed outlier: 6.373A pdb=" N SER C 310 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP C 367 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR C 312 " --> pdb=" O ASP C 367 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU C 279 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL C 387 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE C 278 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE C 389 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA9, first strand: chain 'F' and resid 124 through 125 removed outlier: 6.028A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.992A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.992A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 300 through 302 removed outlier: 5.987A pdb=" N LYS F 254 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASN F 292 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 359 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 523 through 525 removed outlier: 3.660A pdb=" N LEU F 525 " --> pdb=" O ALA F 516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 661 through 662 Processing sheet with id=AB6, first strand: chain 'F' and resid 732 through 734 removed outlier: 3.564A pdb=" N ALA F 734 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 732 through 734 removed outlier: 3.564A pdb=" N ALA F 734 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB9, first strand: chain 'F' and resid 862 through 865 removed outlier: 3.617A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 896 through 907 removed outlier: 4.916A pdb=" N PHE F 897 " --> pdb=" O PHE F 985 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE F 985 " --> pdb=" O PHE F 897 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS F 899 " --> pdb=" O GLN F 983 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLN F 983 " --> pdb=" O LYS F 899 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TYR F 901 " --> pdb=" O GLN F 981 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN F 981 " --> pdb=" O TYR F 901 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N TYR F 903 " --> pdb=" O THR F 979 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR F 979 " --> pdb=" O TYR F 903 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 905 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN F 975 " --> pdb=" O CYS F 907 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 997 through 998 983 hydrogen bonds defined for protein. 2756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.72 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3515 1.27 - 1.41: 5751 1.41 - 1.55: 13211 1.55 - 1.69: 38 1.69 - 1.84: 194 Bond restraints: 22709 Sorted by residual: bond pdb=" C21 3PE A1907 " pdb=" O21 3PE A1907 " ideal model delta sigma weight residual 1.316 1.459 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C21 3PE A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.456 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C21 3PE A1913 " pdb=" O21 3PE A1913 " ideal model delta sigma weight residual 1.316 1.456 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C21 3PE A1912 " pdb=" O21 3PE A1912 " ideal model delta sigma weight residual 1.316 1.456 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C21 3PE A1906 " pdb=" O21 3PE A1906 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.79e+01 ... (remaining 22704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 29100 3.04 - 6.07: 1385 6.07 - 9.11: 181 9.11 - 12.14: 34 12.14 - 15.18: 31 Bond angle restraints: 30731 Sorted by residual: angle pdb=" N ILE A 106 " pdb=" CA ILE A 106 " pdb=" C ILE A 106 " ideal model delta sigma weight residual 111.56 100.82 10.74 8.60e-01 1.35e+00 1.56e+02 angle pdb=" N HIS F 867 " pdb=" CA HIS F 867 " pdb=" C HIS F 867 " ideal model delta sigma weight residual 111.28 122.21 -10.93 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 111.28 121.86 -10.58 1.09e+00 8.42e-01 9.43e+01 angle pdb=" N LYS F 991 " pdb=" CA LYS F 991 " pdb=" C LYS F 991 " ideal model delta sigma weight residual 111.28 119.94 -8.66 1.09e+00 8.42e-01 6.31e+01 angle pdb=" N ASN F 325 " pdb=" CA ASN F 325 " pdb=" C ASN F 325 " ideal model delta sigma weight residual 111.71 120.82 -9.11 1.15e+00 7.56e-01 6.28e+01 ... (remaining 30726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.84: 12642 31.84 - 63.68: 690 63.68 - 95.52: 56 95.52 - 127.37: 2 127.37 - 159.21: 5 Dihedral angle restraints: 13395 sinusoidal: 5496 harmonic: 7899 Sorted by residual: dihedral pdb=" CB CYS F 406 " pdb=" SG CYS F 406 " pdb=" SG CYS F1074 " pdb=" CB CYS F1074 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS F 907 " pdb=" SG CYS F 907 " pdb=" SG CYS F 977 " pdb=" CB CYS F 977 " ideal model delta sinusoidal sigma weight residual 93.00 174.05 -81.05 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS F 844 " pdb=" SG CYS F 844 " pdb=" SG CYS F 853 " pdb=" CB CYS F 853 " ideal model delta sinusoidal sigma weight residual -86.00 -162.01 76.01 1 1.00e+01 1.00e-02 7.28e+01 ... (remaining 13392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.766: 3496 0.766 - 1.531: 2 1.531 - 2.297: 0 2.297 - 3.063: 1 3.063 - 3.828: 1 Chirality restraints: 3500 Sorted by residual: chirality pdb=" C1 NAG L 3 " pdb=" O3 NAG L 2 " pdb=" C2 NAG L 3 " pdb=" O5 NAG L 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.03e+03 chirality pdb=" C1 NAG F1120 " pdb=" ND2 ASN F 784 " pdb=" C2 NAG F1120 " pdb=" O5 NAG F1120 " both_signs ideal model delta sigma weight residual False -2.40 1.43 -3.83 2.00e-01 2.50e+01 3.66e+02 chirality pdb=" C1 NAG D 2 " pdb=" O3 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.90e+02 ... (remaining 3497 not shown) Planarity restraints: 3826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG L 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.345 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG D 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1104 " -0.314 2.00e-02 2.50e+03 2.66e-01 8.85e+02 pdb=" C7 NAG F1104 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F1104 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG F1104 " 0.461 2.00e-02 2.50e+03 pdb=" O7 NAG F1104 " -0.042 2.00e-02 2.50e+03 ... (remaining 3823 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 184 2.52 - 3.11: 16770 3.11 - 3.71: 33006 3.71 - 4.30: 48958 4.30 - 4.90: 79223 Nonbonded interactions: 178141 Sorted by model distance: nonbonded pdb=" O ASN F 480 " pdb=" ND2 ASN F 480 " model vdw 1.921 3.120 nonbonded pdb=" O ARG A 247 " pdb=" OG1 THR A 248 " model vdw 2.051 3.040 nonbonded pdb=" OD1 ASN F 891 " pdb=" O5 NAG F1107 " model vdw 2.082 3.040 nonbonded pdb=" O GLY A 109 " pdb=" O PHE A 110 " model vdw 2.152 3.040 nonbonded pdb=" O GLY F 521 " pdb=" OD1 ASP F 562 " model vdw 2.208 3.040 ... (remaining 178136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.940 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 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 : 0.017 0.916 22746 Z= 0.938 Angle : 1.814 57.986 30826 Z= 0.992 Chirality : 0.121 3.828 3500 Planarity : 0.013 0.300 3813 Dihedral : 17.727 159.206 8246 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 38.36 Ramachandran Plot: Outliers : 1.69 % Allowed : 8.77 % Favored : 89.54 % Rotamer: Outliers : 11.40 % Allowed : 10.92 % Favored : 77.69 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.82 % 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: -3.83 (0.14), residues: 2659 helix: -2.70 (0.12), residues: 1280 sheet: -1.26 (0.34), residues: 214 loop : -2.47 (0.16), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG F 275 TYR 0.060 0.003 TYR F 762 PHE 0.042 0.003 PHE F 663 TRP 0.044 0.004 TRP E 32 HIS 0.017 0.002 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01322 / 0.67 (22709) covalent geometry : angle 1.52194 / 0.91 (30731) SS BOND : bond 0.37520 / 23.93 ( 13) SS BOND : angle 23.89066 / 14.84 ( 26) hydrogen bonds : bond 0.25859 / 16.85 ( 963) hydrogen bonds : angle 9.36929 / 6.47 ( 2756) Misc. bond : bond 0.58169 / 30.62 ( 1) link_BETA1-3 : bond 0.00302 / 0.15 ( 3) link_BETA1-3 : angle 11.49162 / 7.89 ( 9) link_BETA1-4 : bond 0.04691 / 3.71 ( 7) link_BETA1-4 : angle 15.31464 / 8.29 ( 21) link_NAG-ASN : bond 0.22633 / 15.96 ( 13) link_NAG-ASN : angle 15.42392 / 9.47 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 366 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 117 TYR cc_start: 0.4273 (OUTLIER) cc_final: 0.2932 (p90) REVERT: A 135 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.6084 (t80) REVERT: A 284 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8350 (t) REVERT: A 296 ASP cc_start: 0.7977 (m-30) cc_final: 0.7628 (m-30) REVERT: A 516 SER cc_start: 0.3937 (OUTLIER) cc_final: 0.3472 (m) REVERT: A 919 GLN cc_start: 0.3337 (OUTLIER) cc_final: 0.3012 (tp-100) REVERT: A 962 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7595 (mmtt) REVERT: A 964 THR cc_start: 0.8555 (m) cc_final: 0.8284 (m) REVERT: A 1256 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 1318 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7945 (ttt180) REVERT: E 219 GLU cc_start: 0.5141 (OUTLIER) cc_final: 0.3677 (pt0) REVERT: F 133 LEU cc_start: 0.4067 (OUTLIER) cc_final: 0.3525 (mt) REVERT: F 254 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7716 (pttm) REVERT: F 281 MET cc_start: 0.8402 (tpp) cc_final: 0.8113 (OUTLIER) REVERT: F 361 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.6808 (ptp) outliers start: 263 outliers final: 44 residues processed: 562 average time/residue: 0.5487 time to fit residues: 358.6554 Evaluate side-chains 278 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 584 ARG Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 744 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN A 143 ASN A 274 HIS A 277 ASN A 327 ASN A 454 HIS A 599 ASN A 654 ASN A 797 ASN A 829 ASN A 909 ASN ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 ASN A1105 ASN A1131 ASN A1142 GLN A1355 ASN A1464 ASN E 38 HIS E 50 HIS F 56 GLN F 108 GLN F 228 ASN F 357 ASN F 395 ASN F 450 ASN F 511 ASN F 520 ASN F 542 ASN F 687 ASN F 697 ASN F 706 ASN F 866 ASN F1065 ASN F1066 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.230530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.161437 restraints weight = 40796.255| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.93 r_work: 0.3645 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22746 Z= 0.177 Angle : 0.902 17.031 30826 Z= 0.431 Chirality : 0.054 0.732 3500 Planarity : 0.006 0.063 3813 Dihedral : 14.007 162.137 3333 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.74 % Favored : 94.96 % Rotamer: Outliers : 5.98 % Allowed : 17.11 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -2.31 (0.15), residues: 2659 helix: -1.17 (0.13), residues: 1288 sheet: -1.11 (0.30), residues: 278 loop : -1.95 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1389 TYR 0.029 0.002 TYR F 629 PHE 0.020 0.002 PHE E 182 TRP 0.030 0.002 TRP E 32 HIS 0.005 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (22709) covalent geometry : angle 0.86140 / 0.42 (30731) SS BOND : bond 0.00874 / 0.53 ( 13) SS BOND : angle 2.81334 / 1.86 ( 26) hydrogen bonds : bond 0.05329 / 3.47 ( 963) hydrogen bonds : angle 5.39354 / 3.72 ( 2756) Misc. bond : bond 0.00420 / 0.22 ( 1) link_BETA1-3 : bond 0.01222 / 0.60 ( 3) link_BETA1-3 : angle 1.79991 / 1.06 ( 9) link_BETA1-4 : bond 0.00243 / 0.14 ( 7) link_BETA1-4 : angle 3.91647 / 2.21 ( 21) link_NAG-ASN : bond 0.00965 / 0.74 ( 13) link_NAG-ASN : angle 6.63771 / 4.33 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 278 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8606 (mtp) cc_final: 0.8305 (mtp) REVERT: A 165 ARG cc_start: 0.6930 (mtm180) cc_final: 0.6673 (mtm110) REVERT: A 196 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 445 ASN cc_start: 0.7224 (t0) cc_final: 0.6839 (t0) REVERT: A 535 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6312 (pt) REVERT: A 552 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7804 (mm) REVERT: A 553 LEU cc_start: 0.7989 (mt) cc_final: 0.7770 (mt) REVERT: A 883 MET cc_start: 0.2408 (ppp) cc_final: 0.1412 (tpt) REVERT: A 919 GLN cc_start: 0.2287 (OUTLIER) cc_final: 0.1566 (tp-100) REVERT: A 921 VAL cc_start: 0.5420 (OUTLIER) cc_final: 0.5086 (m) REVERT: A 962 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8303 (mptt) REVERT: A 1236 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7039 (mtp85) REVERT: A 1256 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8586 (tp) REVERT: A 1318 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8346 (ttt180) REVERT: E 51 PHE cc_start: 0.5009 (m-80) cc_final: 0.4275 (m-10) REVERT: E 213 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7269 (mt-10) REVERT: C 274 MET cc_start: 0.0159 (tmm) cc_final: -0.0181 (mmm) REVERT: C 422 LEU cc_start: -0.0116 (OUTLIER) cc_final: -0.0695 (pp) REVERT: F 55 HIS cc_start: 0.6698 (OUTLIER) cc_final: 0.6305 (t-90) REVERT: F 361 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8146 (mtt) REVERT: F 457 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: F 593 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7817 (mp) REVERT: F 651 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6657 (pt) REVERT: F 849 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.6858 (t0) REVERT: F 867 HIS cc_start: 0.6298 (OUTLIER) cc_final: 0.5426 (m-70) outliers start: 138 outliers final: 35 residues processed: 381 average time/residue: 0.4751 time to fit residues: 214.3687 Evaluate side-chains 279 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 919 GLN Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 337 LYS Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 457 GLU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 532 LYS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 900 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 2 optimal weight: 6.9990 chunk 179 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 222 optimal weight: 0.3980 chunk 257 optimal weight: 0.0970 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN F 308 HIS F 477 ASN F 480 ASN F 570 ASN ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 716 ASN F 720 GLN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.228027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158614 restraints weight = 29401.826| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.86 r_work: 0.3523 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22746 Z= 0.141 Angle : 0.754 17.075 30826 Z= 0.360 Chirality : 0.048 0.526 3500 Planarity : 0.005 0.058 3813 Dihedral : 12.373 175.076 3268 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.93 % Favored : 94.81 % Rotamer: Outliers : 4.77 % Allowed : 19.28 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2659 helix: -0.38 (0.14), residues: 1308 sheet: -0.87 (0.32), residues: 250 loop : -1.68 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F1032 TYR 0.026 0.002 TYR F 629 PHE 0.021 0.002 PHE E 189 TRP 0.024 0.001 TRP E 32 HIS 0.004 0.001 HIS A1397 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (22709) covalent geometry : angle 0.72541 / 0.35 (30731) SS BOND : bond 0.00336 / 0.22 ( 13) SS BOND : angle 2.55359 / 1.51 ( 26) hydrogen bonds : bond 0.04466 / 2.90 ( 963) hydrogen bonds : angle 4.83160 / 3.32 ( 2756) Misc. bond : bond 0.00183 / 0.10 ( 1) link_BETA1-3 : bond 0.00653 / 0.33 ( 3) link_BETA1-3 : angle 1.61991 / 1.02 ( 9) link_BETA1-4 : bond 0.00353 / 0.23 ( 7) link_BETA1-4 : angle 2.56016 / 1.49 ( 21) link_NAG-ASN : bond 0.00869 / 0.65 ( 13) link_NAG-ASN : angle 5.12944 / 3.44 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 238 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.6468 (ttm110) cc_final: 0.5781 (ttt180) REVERT: A 260 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.6312 (pm20) REVERT: A 479 MET cc_start: 0.5297 (tmt) cc_final: 0.4485 (tpt) REVERT: A 483 MET cc_start: 0.3457 (tpt) cc_final: 0.3005 (tmm) REVERT: A 493 MET cc_start: 0.5669 (tpp) cc_final: 0.5076 (mpp) REVERT: A 883 MET cc_start: 0.2819 (ppp) cc_final: 0.1651 (tpt) REVERT: A 900 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6364 (tmm160) REVERT: A 1005 MET cc_start: 0.9351 (tpt) cc_final: 0.8982 (tpt) REVERT: A 1063 PHE cc_start: 0.6880 (t80) cc_final: 0.6582 (t80) REVERT: A 1236 ARG cc_start: 0.7891 (mtm110) cc_final: 0.7411 (mtp85) REVERT: A 1318 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.7916 (ttm-80) REVERT: E 21 VAL cc_start: 0.6837 (t) cc_final: 0.6625 (p) REVERT: E 51 PHE cc_start: 0.4837 (m-80) cc_final: 0.3998 (m-10) REVERT: E 129 PHE cc_start: 0.4967 (t80) cc_final: 0.4340 (t80) REVERT: E 142 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6329 (mtp) REVERT: E 158 MET cc_start: 0.5807 (mmt) cc_final: 0.5329 (mmm) REVERT: E 182 PHE cc_start: 0.4276 (OUTLIER) cc_final: 0.4029 (m-10) REVERT: E 213 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7234 (mt-10) REVERT: C 422 LEU cc_start: -0.0355 (OUTLIER) cc_final: -0.0897 (pp) REVERT: F 182 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8378 (mp) REVERT: F 361 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8089 (mtt) REVERT: F 506 PHE cc_start: 0.8288 (m-80) cc_final: 0.8006 (m-10) REVERT: F 530 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: F 651 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6870 (pt) REVERT: F 1068 LEU cc_start: 0.7637 (pp) cc_final: 0.7394 (tp) outliers start: 110 outliers final: 35 residues processed: 323 average time/residue: 0.4966 time to fit residues: 189.3024 Evaluate side-chains 266 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1074 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 144 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 218 optimal weight: 0.5980 chunk 226 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 797 ASN ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN A1148 HIS E 209 GLN ** F 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 706 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.222829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.155053 restraints weight = 35627.705| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.49 r_work: 0.3472 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22746 Z= 0.186 Angle : 0.779 16.023 30826 Z= 0.372 Chirality : 0.049 0.482 3500 Planarity : 0.006 0.066 3813 Dihedral : 11.974 173.961 3255 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.74 % Favored : 95.03 % Rotamer: Outliers : 4.51 % Allowed : 19.54 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2659 helix: -0.01 (0.14), residues: 1317 sheet: -0.61 (0.31), residues: 262 loop : -1.57 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 385 TYR 0.026 0.002 TYR F 601 PHE 0.039 0.002 PHE F 469 TRP 0.017 0.002 TRP E 32 HIS 0.010 0.001 HIS C 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (22709) covalent geometry : angle 0.75572 / 0.37 (30731) SS BOND : bond 0.01254 / 0.68 ( 13) SS BOND : angle 2.19056 / 1.28 ( 26) hydrogen bonds : bond 0.04869 / 3.18 ( 963) hydrogen bonds : angle 4.70978 / 3.23 ( 2756) Misc. bond : bond 0.00276 / 0.15 ( 1) link_BETA1-3 : bond 0.00768 / 0.38 ( 3) link_BETA1-3 : angle 1.43929 / 0.89 ( 9) link_BETA1-4 : bond 0.00339 / 0.21 ( 7) link_BETA1-4 : angle 2.64699 / 1.56 ( 21) link_NAG-ASN : bond 0.00811 / 0.59 ( 13) link_NAG-ASN : angle 4.69038 / 3.18 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 243 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6778 (tp30) REVERT: A 170 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8259 (mp) REVERT: A 196 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8342 (mp) REVERT: A 479 MET cc_start: 0.5329 (tmt) cc_final: 0.4561 (tpt) REVERT: A 483 MET cc_start: 0.2883 (tpt) cc_final: 0.2616 (tmm) REVERT: A 535 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6317 (pt) REVERT: A 557 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7165 (ttm-80) REVERT: A 636 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 806 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5915 (mt) REVERT: A 823 ARG cc_start: 0.7186 (ptp90) cc_final: 0.6933 (ptp-170) REVERT: A 883 MET cc_start: 0.2682 (ppp) cc_final: 0.1632 (tpt) REVERT: A 900 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6354 (tmm160) REVERT: A 1236 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7469 (mtp85) REVERT: A 1318 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8480 (ttt180) REVERT: A 1321 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.7792 (p) REVERT: E 21 VAL cc_start: 0.6874 (t) cc_final: 0.6646 (p) REVERT: E 127 MET cc_start: 0.4800 (OUTLIER) cc_final: 0.4593 (tmt) REVERT: E 213 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7076 (mt-10) REVERT: C 422 LEU cc_start: -0.0544 (OUTLIER) cc_final: -0.0980 (pp) REVERT: F 283 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8359 (mm-30) REVERT: F 361 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8171 (mtt) REVERT: F 451 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8857 (t) REVERT: F 530 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: F 651 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6777 (pt) REVERT: F 1050 VAL cc_start: 0.5183 (OUTLIER) cc_final: 0.4829 (t) REVERT: F 1068 LEU cc_start: 0.7975 (pp) cc_final: 0.7653 (tp) outliers start: 104 outliers final: 39 residues processed: 327 average time/residue: 0.5000 time to fit residues: 192.3877 Evaluate side-chains 284 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 930 ASN Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1393 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1050 VAL Chi-restraints excluded: chain F residue 1074 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 266 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 ASN F 679 ASN F 706 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.223707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.156712 restraints weight = 40790.452| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 4.31 r_work: 0.3453 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22746 Z= 0.140 Angle : 0.708 15.885 30826 Z= 0.336 Chirality : 0.046 0.457 3500 Planarity : 0.005 0.067 3813 Dihedral : 11.629 176.523 3252 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.78 % Favored : 95.03 % Rotamer: Outliers : 3.86 % Allowed : 20.36 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.16), residues: 2659 helix: 0.33 (0.14), residues: 1327 sheet: -0.31 (0.32), residues: 251 loop : -1.44 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 247 TYR 0.023 0.001 TYR F 629 PHE 0.017 0.001 PHE F 469 TRP 0.012 0.001 TRP F 207 HIS 0.005 0.001 HIS C 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (22709) covalent geometry : angle 0.67988 / 0.33 (30731) SS BOND : bond 0.00267 / 0.19 ( 13) SS BOND : angle 1.92447 / 1.20 ( 26) hydrogen bonds : bond 0.04213 / 2.76 ( 963) hydrogen bonds : angle 4.51808 / 3.11 ( 2756) Misc. bond : bond 0.00076 / 0.04 ( 1) link_BETA1-3 : bond 0.00780 / 0.39 ( 3) link_BETA1-3 : angle 1.34689 / 0.83 ( 9) link_BETA1-4 : bond 0.00385 / 0.26 ( 7) link_BETA1-4 : angle 2.41145 / 1.45 ( 21) link_NAG-ASN : bond 0.01099 / 0.82 ( 13) link_NAG-ASN : angle 5.12486 / 3.30 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 231 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7869 (tm-30) cc_final: 0.6984 (tp30) REVERT: A 170 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8275 (mp) REVERT: A 260 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: A 479 MET cc_start: 0.5326 (tmt) cc_final: 0.4526 (tpt) REVERT: A 483 MET cc_start: 0.2909 (tpt) cc_final: 0.2622 (tmm) REVERT: A 535 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6257 (pt) REVERT: A 806 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5864 (mt) REVERT: A 823 ARG cc_start: 0.7185 (ptp90) cc_final: 0.6931 (ptp-170) REVERT: A 883 MET cc_start: 0.2585 (ppp) cc_final: 0.1593 (tpt) REVERT: A 900 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6311 (tmm160) REVERT: A 1005 MET cc_start: 0.9247 (tpt) cc_final: 0.8890 (tpt) REVERT: A 1318 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8364 (ttt180) REVERT: E 21 VAL cc_start: 0.6894 (t) cc_final: 0.6667 (p) REVERT: E 127 MET cc_start: 0.4925 (OUTLIER) cc_final: 0.4717 (tmt) REVERT: E 213 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7280 (mt-10) REVERT: C 422 LEU cc_start: -0.0561 (OUTLIER) cc_final: -0.1018 (pp) REVERT: F 283 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8392 (mm-30) REVERT: F 361 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8151 (mtt) REVERT: F 530 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: F 534 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8109 (pp) REVERT: F 651 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6733 (pt) REVERT: F 1049 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5829 (mtm) outliers start: 89 outliers final: 36 residues processed: 302 average time/residue: 0.5053 time to fit residues: 179.5325 Evaluate side-chains 273 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 891 ASN Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 1049 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 11 optimal weight: 2.9990 chunk 187 optimal weight: 0.0270 chunk 232 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 245 optimal weight: 0.0020 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 930 ASN E 209 GLN F 706 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.222440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.153732 restraints weight = 39003.136| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 4.05 r_work: 0.3408 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22746 Z= 0.146 Angle : 0.707 15.121 30826 Z= 0.335 Chirality : 0.047 0.478 3500 Planarity : 0.005 0.058 3813 Dihedral : 11.505 171.721 3250 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.93 % Favored : 94.88 % Rotamer: Outliers : 4.07 % Allowed : 20.58 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2659 helix: 0.61 (0.14), residues: 1329 sheet: -0.31 (0.32), residues: 263 loop : -1.32 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 247 TYR 0.024 0.002 TYR F 629 PHE 0.022 0.002 PHE F 469 TRP 0.014 0.001 TRP E 32 HIS 0.005 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (22709) covalent geometry : angle 0.67897 / 0.33 (30731) SS BOND : bond 0.00324 / 0.21 ( 13) SS BOND : angle 2.08711 / 1.17 ( 26) hydrogen bonds : bond 0.04219 / 2.77 ( 963) hydrogen bonds : angle 4.45293 / 3.06 ( 2756) Misc. bond : bond 0.00312 / 0.16 ( 1) link_BETA1-3 : bond 0.00710 / 0.35 ( 3) link_BETA1-3 : angle 1.34573 / 0.84 ( 9) link_BETA1-4 : bond 0.00345 / 0.23 ( 7) link_BETA1-4 : angle 2.51582 / 1.49 ( 21) link_NAG-ASN : bond 0.01062 / 0.80 ( 13) link_NAG-ASN : angle 5.02702 / 3.18 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 229 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9132 (mtp) cc_final: 0.8920 (mtt) REVERT: A 90 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: A 164 LEU cc_start: 0.8373 (tp) cc_final: 0.8133 (tp) REVERT: A 196 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 479 MET cc_start: 0.5319 (tmt) cc_final: 0.4537 (tpt) REVERT: A 483 MET cc_start: 0.3075 (tpt) cc_final: 0.2784 (tmm) REVERT: A 535 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6189 (pt) REVERT: A 557 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7299 (ttm-80) REVERT: A 806 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5902 (mt) REVERT: A 823 ARG cc_start: 0.7310 (ptp90) cc_final: 0.7045 (ptp-170) REVERT: A 883 MET cc_start: 0.2545 (ppp) cc_final: 0.1597 (tpt) REVERT: A 902 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6874 (pp) REVERT: A 1005 MET cc_start: 0.9271 (tpt) cc_final: 0.8930 (tpt) REVERT: A 1287 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7894 (mp-120) REVERT: A 1318 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.7764 (ttm-80) REVERT: A 1321 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.7769 (p) REVERT: A 1475 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.5012 (pt) REVERT: E 51 PHE cc_start: 0.5017 (OUTLIER) cc_final: 0.4445 (m-80) REVERT: E 206 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6609 (ptt90) REVERT: E 209 GLN cc_start: 0.6921 (mt0) cc_final: 0.6210 (mp10) REVERT: E 213 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7430 (mt-10) REVERT: C 422 LEU cc_start: -0.0228 (OUTLIER) cc_final: -0.0756 (pp) REVERT: F 283 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8530 (mm-30) REVERT: F 325 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8878 (m-40) REVERT: F 361 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8363 (mtt) REVERT: F 530 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: F 651 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6757 (pt) outliers start: 94 outliers final: 43 residues processed: 303 average time/residue: 0.5242 time to fit residues: 187.2314 Evaluate side-chains 278 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1393 ILE Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain E residue 51 PHE Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 518 ASP Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 900 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 129 optimal weight: 0.9990 chunk 260 optimal weight: 6.9990 chunk 69 optimal weight: 0.2980 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 0.1980 chunk 114 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 930 ASN F 706 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.223953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.156355 restraints weight = 39040.289| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.70 r_work: 0.3489 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22746 Z= 0.114 Angle : 0.661 14.662 30826 Z= 0.311 Chirality : 0.044 0.480 3500 Planarity : 0.004 0.055 3813 Dihedral : 11.207 173.831 3245 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.26 % Rotamer: Outliers : 3.34 % Allowed : 21.49 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2659 helix: 0.87 (0.14), residues: 1324 sheet: -0.23 (0.32), residues: 263 loop : -1.22 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 247 TYR 0.026 0.001 TYR F 629 PHE 0.014 0.001 PHE F 878 TRP 0.013 0.001 TRP F 187 HIS 0.005 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (22709) covalent geometry : angle 0.63462 / 0.30 (30731) SS BOND : bond 0.00183 / 0.13 ( 13) SS BOND : angle 1.69867 / 1.02 ( 26) hydrogen bonds : bond 0.03653 / 2.40 ( 963) hydrogen bonds : angle 4.31788 / 2.97 ( 2756) Misc. bond : bond 0.00888 / 0.47 ( 1) link_BETA1-3 : bond 0.00694 / 0.34 ( 3) link_BETA1-3 : angle 1.28032 / 0.78 ( 9) link_BETA1-4 : bond 0.00417 / 0.28 ( 7) link_BETA1-4 : angle 2.32277 / 1.40 ( 21) link_NAG-ASN : bond 0.01033 / 0.76 ( 13) link_NAG-ASN : angle 4.80303 / 3.10 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 226 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9076 (mtp) cc_final: 0.8857 (mtt) REVERT: A 90 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7054 (tp30) REVERT: A 164 LEU cc_start: 0.8158 (tp) cc_final: 0.7913 (tp) REVERT: A 247 ARG cc_start: 0.6777 (ttm110) cc_final: 0.6189 (ttt180) REVERT: A 479 MET cc_start: 0.5246 (tmt) cc_final: 0.4157 (tpp) REVERT: A 535 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6175 (pt) REVERT: A 557 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7267 (ttm-80) REVERT: A 806 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5935 (mt) REVERT: A 883 MET cc_start: 0.2424 (ppp) cc_final: 0.1435 (tpt) REVERT: A 1005 MET cc_start: 0.9197 (tpt) cc_final: 0.8797 (tpt) REVERT: A 1287 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7701 (mp-120) REVERT: A 1318 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.7810 (ttt180) REVERT: A 1475 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4980 (pt) REVERT: E 34 VAL cc_start: 0.5187 (t) cc_final: 0.4974 (t) REVERT: E 158 MET cc_start: 0.6050 (tpp) cc_final: 0.5472 (tpp) REVERT: E 206 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6593 (ptt90) REVERT: E 209 GLN cc_start: 0.6797 (mt0) cc_final: 0.6110 (mp10) REVERT: E 213 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7238 (mt-10) REVERT: C 366 LEU cc_start: 0.1911 (mt) cc_final: 0.1648 (tp) REVERT: C 422 LEU cc_start: -0.0470 (OUTLIER) cc_final: -0.0936 (pp) REVERT: F 199 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8345 (ttm-80) REVERT: F 283 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8429 (mm-30) REVERT: F 325 ASN cc_start: 0.9029 (m110) cc_final: 0.8820 (m-40) REVERT: F 361 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7937 (mtt) REVERT: F 530 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: F 570 ASN cc_start: 0.7542 (m-40) cc_final: 0.7164 (m110) REVERT: F 651 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6721 (pt) REVERT: F 1049 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.5842 (mtm) outliers start: 77 outliers final: 34 residues processed: 287 average time/residue: 0.4917 time to fit residues: 167.5881 Evaluate side-chains 267 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1393 ILE Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 518 ASP Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 819 ILE Chi-restraints excluded: chain F residue 891 ASN Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1049 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 208 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 45 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 139 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 930 ASN F 484 GLN F 706 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.223922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156515 restraints weight = 37566.630| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.28 r_work: 0.3480 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22746 Z= 0.113 Angle : 0.660 14.275 30826 Z= 0.309 Chirality : 0.044 0.483 3500 Planarity : 0.004 0.052 3813 Dihedral : 10.844 173.597 3245 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.07 % Rotamer: Outliers : 2.99 % Allowed : 22.40 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2659 helix: 1.04 (0.14), residues: 1324 sheet: -0.31 (0.31), residues: 280 loop : -1.17 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 247 TYR 0.026 0.001 TYR F 629 PHE 0.029 0.001 PHE E 182 TRP 0.013 0.001 TRP E 32 HIS 0.004 0.001 HIS C 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (22709) covalent geometry : angle 0.63584 / 0.30 (30731) SS BOND : bond 0.00173 / 0.12 ( 13) SS BOND : angle 1.51158 / 0.90 ( 26) hydrogen bonds : bond 0.03548 / 2.33 ( 963) hydrogen bonds : angle 4.25641 / 2.93 ( 2756) Misc. bond : bond 0.00154 / 0.08 ( 1) link_BETA1-3 : bond 0.00755 / 0.37 ( 3) link_BETA1-3 : angle 1.30167 / 0.79 ( 9) link_BETA1-4 : bond 0.00364 / 0.25 ( 7) link_BETA1-4 : angle 2.28200 / 1.37 ( 21) link_NAG-ASN : bond 0.00946 / 0.71 ( 13) link_NAG-ASN : angle 4.61640 / 2.98 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 219 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8155 (mp) cc_final: 0.7933 (mm) REVERT: A 90 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7061 (tp30) REVERT: A 164 LEU cc_start: 0.8139 (tp) cc_final: 0.7908 (tp) REVERT: A 479 MET cc_start: 0.5111 (tmt) cc_final: 0.4180 (tpp) REVERT: A 483 MET cc_start: 0.3407 (tpp) cc_final: 0.3198 (tmm) REVERT: A 493 MET cc_start: 0.4854 (mtm) cc_final: 0.4500 (mpp) REVERT: A 535 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6222 (pt) REVERT: A 553 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7727 (mt) REVERT: A 557 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7193 (ttm-80) REVERT: A 636 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8819 (mp) REVERT: A 806 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6110 (mt) REVERT: A 883 MET cc_start: 0.2236 (ppp) cc_final: 0.1397 (tpt) REVERT: A 921 VAL cc_start: 0.5250 (OUTLIER) cc_final: 0.4896 (m) REVERT: A 1005 MET cc_start: 0.9200 (tpt) cc_final: 0.8806 (tpt) REVERT: A 1287 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7662 (mp-120) REVERT: A 1318 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7891 (ttt180) REVERT: A 1475 LEU cc_start: 0.5074 (OUTLIER) cc_final: 0.4867 (pt) REVERT: E 206 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6604 (ptt90) REVERT: E 209 GLN cc_start: 0.6771 (mt0) cc_final: 0.6116 (mp10) REVERT: E 213 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 366 LEU cc_start: 0.2154 (mt) cc_final: 0.1821 (tp) REVERT: C 422 LEU cc_start: -0.0225 (OUTLIER) cc_final: -0.0749 (pp) REVERT: F 152 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7508 (pt) REVERT: F 199 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8298 (ttt90) REVERT: F 283 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8434 (mm-30) REVERT: F 325 ASN cc_start: 0.9016 (m110) cc_final: 0.8801 (m-40) REVERT: F 530 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: F 570 ASN cc_start: 0.7571 (m-40) cc_final: 0.7365 (m-40) REVERT: F 651 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6727 (pt) outliers start: 69 outliers final: 35 residues processed: 276 average time/residue: 0.4960 time to fit residues: 161.4251 Evaluate side-chains 268 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1393 ILE Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 518 ASP Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 125 optimal weight: 50.0000 chunk 29 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 264 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 930 ASN F 706 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.219707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143113 restraints weight = 28240.412| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.61 r_work: 0.3346 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 22746 Z= 0.219 Angle : 0.773 14.015 30826 Z= 0.370 Chirality : 0.049 0.498 3500 Planarity : 0.005 0.074 3813 Dihedral : 11.355 152.889 3240 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.78 % Favored : 95.07 % Rotamer: Outliers : 3.51 % Allowed : 21.79 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2659 helix: 0.76 (0.14), residues: 1331 sheet: -0.20 (0.32), residues: 260 loop : -1.28 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 247 TYR 0.023 0.002 TYR F 762 PHE 0.033 0.002 PHE F 469 TRP 0.019 0.002 TRP A1406 HIS 0.006 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (22709) covalent geometry : angle 0.75066 / 0.36 (30731) SS BOND : bond 0.00381 / 0.23 ( 13) SS BOND : angle 2.07937 / 1.25 ( 26) hydrogen bonds : bond 0.05031 / 3.29 ( 963) hydrogen bonds : angle 4.49481 / 3.09 ( 2756) Misc. bond : bond 0.00100 / 0.05 ( 1) link_BETA1-3 : bond 0.00743 / 0.36 ( 3) link_BETA1-3 : angle 1.29146 / 0.81 ( 9) link_BETA1-4 : bond 0.00355 / 0.23 ( 7) link_BETA1-4 : angle 2.56816 / 1.56 ( 21) link_NAG-ASN : bond 0.01021 / 0.76 ( 13) link_NAG-ASN : angle 4.68900 / 3.08 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 228 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: A 247 ARG cc_start: 0.6966 (ttm110) cc_final: 0.6472 (ttt180) REVERT: A 479 MET cc_start: 0.4657 (tmt) cc_final: 0.4353 (tpp) REVERT: A 483 MET cc_start: 0.3491 (tpp) cc_final: 0.3184 (tmm) REVERT: A 553 LEU cc_start: 0.8434 (mm) cc_final: 0.7963 (mt) REVERT: A 557 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7534 (ttm-80) REVERT: A 636 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8947 (mp) REVERT: A 662 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7418 (t0) REVERT: A 806 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6264 (mt) REVERT: A 883 MET cc_start: 0.2246 (ppp) cc_final: 0.1429 (tpt) REVERT: A 921 VAL cc_start: 0.5252 (OUTLIER) cc_final: 0.4892 (m) REVERT: A 1052 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8685 (mm) REVERT: A 1287 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8134 (mp-120) REVERT: A 1318 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8551 (ttt180) REVERT: A 1475 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.5132 (pt) REVERT: E 9 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6562 (t) REVERT: E 34 VAL cc_start: 0.4991 (t) cc_final: 0.4757 (t) REVERT: E 152 PHE cc_start: 0.6727 (t80) cc_final: 0.6282 (t80) REVERT: E 206 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6695 (ptt90) REVERT: E 209 GLN cc_start: 0.6937 (mt0) cc_final: 0.6191 (mp10) REVERT: E 213 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7372 (mt-10) REVERT: C 366 LEU cc_start: 0.2156 (mt) cc_final: 0.1843 (tp) REVERT: C 422 LEU cc_start: -0.0184 (OUTLIER) cc_final: -0.0697 (pp) REVERT: F 199 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8432 (ttt90) REVERT: F 325 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8920 (m-40) REVERT: F 451 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8883 (t) REVERT: F 530 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: F 534 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8251 (pp) REVERT: F 651 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6814 (pt) outliers start: 81 outliers final: 35 residues processed: 287 average time/residue: 0.4986 time to fit residues: 169.3922 Evaluate side-chains 270 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1393 ILE Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 518 ASP Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 31 optimal weight: 9.9990 chunk 243 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 252 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 930 ASN F 706 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.221660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.150310 restraints weight = 30732.224| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.99 r_work: 0.3375 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22746 Z= 0.128 Angle : 0.697 13.086 30826 Z= 0.327 Chirality : 0.045 0.480 3500 Planarity : 0.004 0.053 3813 Dihedral : 10.996 152.007 3240 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 2.64 % Allowed : 22.70 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.16), residues: 2659 helix: 1.01 (0.14), residues: 1320 sheet: -0.10 (0.33), residues: 259 loop : -1.23 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 247 TYR 0.024 0.001 TYR F 629 PHE 0.033 0.001 PHE E 182 TRP 0.013 0.001 TRP A1406 HIS 0.004 0.001 HIS C 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (22709) covalent geometry : angle 0.67493 / 0.32 (30731) SS BOND : bond 0.00314 / 0.20 ( 13) SS BOND : angle 1.59073 / 0.94 ( 26) hydrogen bonds : bond 0.03985 / 2.62 ( 963) hydrogen bonds : angle 4.33743 / 2.99 ( 2756) Misc. bond : bond 0.00099 / 0.05 ( 1) link_BETA1-3 : bond 0.00793 / 0.39 ( 3) link_BETA1-3 : angle 1.24416 / 0.76 ( 9) link_BETA1-4 : bond 0.00390 / 0.27 ( 7) link_BETA1-4 : angle 2.35622 / 1.45 ( 21) link_NAG-ASN : bond 0.00926 / 0.69 ( 13) link_NAG-ASN : angle 4.42438 / 2.88 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 0.790 Fit side-chains revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7103 (tp30) REVERT: A 247 ARG cc_start: 0.6934 (ttm110) cc_final: 0.6511 (ttt180) REVERT: A 479 MET cc_start: 0.4616 (tmt) cc_final: 0.4347 (tpp) REVERT: A 483 MET cc_start: 0.3648 (tpp) cc_final: 0.3425 (tmm) REVERT: A 553 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7875 (mt) REVERT: A 557 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7380 (ttm-80) REVERT: A 636 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8880 (mp) REVERT: A 662 ASP cc_start: 0.7555 (t70) cc_final: 0.7269 (t0) REVERT: A 806 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6275 (mt) REVERT: A 883 MET cc_start: 0.2301 (ppp) cc_final: 0.1527 (tpt) REVERT: A 906 ARG cc_start: 0.5503 (OUTLIER) cc_final: 0.5249 (ptp-110) REVERT: A 921 VAL cc_start: 0.5147 (OUTLIER) cc_final: 0.4781 (m) REVERT: A 1005 MET cc_start: 0.9116 (tpt) cc_final: 0.8703 (tpt) REVERT: A 1052 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 1287 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7958 (mp-120) REVERT: A 1318 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.7901 (ttm-80) REVERT: A 1475 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.5170 (pt) REVERT: E 9 VAL cc_start: 0.6889 (p) cc_final: 0.6576 (t) REVERT: E 152 PHE cc_start: 0.6692 (t80) cc_final: 0.6208 (t80) REVERT: E 158 MET cc_start: 0.5709 (tpp) cc_final: 0.5140 (tpt) REVERT: E 206 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6675 (ptt90) REVERT: E 209 GLN cc_start: 0.6813 (mt0) cc_final: 0.6252 (mp10) REVERT: E 213 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7316 (mt-10) REVERT: C 366 LEU cc_start: 0.2183 (mt) cc_final: 0.1805 (tp) REVERT: C 422 LEU cc_start: -0.0209 (OUTLIER) cc_final: -0.0717 (pp) REVERT: F 199 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8218 (ttm-80) REVERT: F 325 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8787 (m-40) REVERT: F 530 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7728 (mt0) REVERT: F 651 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6728 (pt) outliers start: 61 outliers final: 30 residues processed: 277 average time/residue: 0.4860 time to fit residues: 159.1250 Evaluate side-chains 261 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 906 ARG Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1287 GLN Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 GLN Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1393 ILE Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 518 ASP Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 581 ILE Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 891 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 930 ASN F 706 ASN ** F 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 975 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.221569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.152939 restraints weight = 38897.065| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.50 r_work: 0.3403 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22746 Z= 0.126 Angle : 0.693 12.953 30826 Z= 0.325 Chirality : 0.046 0.487 3500 Planarity : 0.004 0.055 3813 Dihedral : 10.859 147.811 3238 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 2.25 % Allowed : 23.44 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.16), residues: 2659 helix: 1.13 (0.14), residues: 1313 sheet: -0.01 (0.33), residues: 259 loop : -1.19 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 247 TYR 0.025 0.001 TYR F 629 PHE 0.028 0.001 PHE E 182 TRP 0.013 0.001 TRP A1406 HIS 0.004 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (22709) covalent geometry : angle 0.67040 / 0.32 (30731) SS BOND : bond 0.00222 / 0.14 ( 13) SS BOND : angle 1.56908 / 0.94 ( 26) hydrogen bonds : bond 0.03876 / 2.55 ( 963) hydrogen bonds : angle 4.28477 / 2.96 ( 2756) Misc. bond : bond 0.00135 / 0.07 ( 1) link_BETA1-3 : bond 0.00945 / 0.46 ( 3) link_BETA1-3 : angle 1.32207 / 0.80 ( 9) link_BETA1-4 : bond 0.00384 / 0.26 ( 7) link_BETA1-4 : angle 2.31239 / 1.42 ( 21) link_NAG-ASN : bond 0.00889 / 0.66 ( 13) link_NAG-ASN : angle 4.58153 / 2.95 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13583.92 seconds wall clock time: 230 minutes 30.94 seconds (13830.94 seconds total)