Starting phenix.real_space_refine on Mon Jul 6 17:01:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z6q_14528/07_2026/7z6q_14528_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z6q_14528/07_2026/7z6q_14528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z6q_14528/07_2026/7z6q_14528_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z6q_14528/07_2026/7z6q_14528_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z6q_14528/07_2026/7z6q_14528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z6q_14528/07_2026/7z6q_14528.map" } resolution = 2.5 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= 0.004 sd= 0.080 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 12 7.16 5 P 4 5.49 5 Mg 78 5.21 5 S 135 5.16 5 C 24607 2.51 5 N 5611 2.21 5 O 6108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36557 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 5344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5344 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 26, 'TRANS': 640} Chain: "B" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain breaks: 1 Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "D" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 970 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Chain: "E" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2798 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 339} Chain: "F" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2798 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 339} Chain: "G" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2798 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 339} Chain: "H" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2790 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 338} Chain: "I" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2798 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 339} Chain: "J" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2783 Classifications: {'peptide': 357} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 337} Chain: "a" Number of atoms: 5230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5230 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 26, 'TRANS': 627} Chain: "c" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 1171 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 21, 1170 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 12, 'CLA': 2, 'F39': 1, 'GS0': 1, 'IKV': 1, 'LHG': 2, 'SF4': 1} Classifications: {'undetermined': 20} Link IDs: {None: 18} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 9, 574 Unusual residues: {'BCL': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 554 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 9, 554 Unusual residues: {'BCL': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 396 Unusual residues: {'BCL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 508 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 8, 508 Unusual residues: {'BCL': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 554 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 9, 554 Unusual residues: {'BCL': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 462 Unusual residues: {'BCL': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "a" Number of atoms: 1163 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 20, 1162 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BCL': 12, 'CLA': 2, 'F39': 1, 'GS0': 1, 'IKV': 1, 'LHG': 2} Classifications: {'undetermined': 19} Link IDs: {None: 18} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28751 SG CYS a 527 68.839 80.462 79.816 1.00 17.80 S ATOM 28810 SG CYS a 536 69.098 84.530 80.976 1.00 19.37 S ATOM 3889 SG CYS A 527 67.780 81.846 85.364 1.00 16.71 S ATOM 3948 SG CYS A 536 64.561 82.828 83.348 1.00 17.48 S ATOM 3948 SG CYS A 536 64.561 82.828 83.348 1.00 17.48 S ATOM 28810 SG CYS a 536 69.098 84.530 80.976 1.00 19.37 S ATOM 5919 SG CYS B 182 86.558 72.488 96.848 1.00 19.28 S ATOM 5899 SG CYS B 179 86.526 66.743 92.796 1.00 18.96 S ATOM 5674 SG CYS B 150 85.590 72.633 90.745 1.00 23.55 S ATOM 5936 SG CYS B 185 80.973 69.946 94.475 1.00 15.98 S ATOM 5980 SG CYS B 191 71.396 69.442 92.555 1.00 14.12 S ATOM 5608 SG CYS B 140 72.975 68.990 85.975 1.00 13.39 S ATOM 5643 SG CYS B 146 76.874 71.850 89.310 1.00 14.43 S ATOM 5625 SG CYS B 143 71.361 74.465 88.711 1.00 19.88 S Time building chain proxies: 8.49, per 1000 atoms: 0.23 Number of scatterers: 36557 At special positions: 0 Unit cell: (112.995, 159.867, 195.021, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 12 26.01 Ca 2 19.99 S 135 16.00 P 4 15.00 Mg 78 11.99 O 6108 8.00 N 5611 7.00 C 24607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=128, symmetry=0 Number of additional bonds: simple=128, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 821 " pdb="FE2 SF4 A 821 " - pdb=" SG CYS A 527 " pdb="FE1 SF4 A 821 " - pdb=" SG CYS a 536 " pdb="FE2 SF4 A 821 " - pdb=" SG CYS A 536 " pdb="FE1 SF4 A 821 " - pdb=" SG CYS a 527 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 179 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 150 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 185 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 182 " pdb=" SF4 B 302 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 146 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 143 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 191 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 140 " Number of angles added : 36 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7152 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 23 sheets defined 40.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.711A pdb=" N PHE A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 50 " --> pdb=" O MET A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 4.024A pdb=" N ILE A 64 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 71 through 91 Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.542A pdb=" N ILE A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.520A pdb=" N THR A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 132 through 166 removed outlier: 3.512A pdb=" N ALA A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.551A pdb=" N ASP A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 227 removed outlier: 3.527A pdb=" N LEU A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Proline residue: A 208 - end of helix removed outlier: 3.560A pdb=" N TRP A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 263 removed outlier: 3.566A pdb=" N ALA A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP A 261 " --> pdb=" O GLY A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 274 through 301 removed outlier: 3.534A pdb=" N ALA A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 299 " --> pdb=" O CYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 402 removed outlier: 3.549A pdb=" N GLY A 380 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.626A pdb=" N ILE A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 417 through 452 removed outlier: 3.804A pdb=" N SER A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 456 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 468 through 475 removed outlier: 4.691A pdb=" N TRP A 473 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 506 removed outlier: 3.539A pdb=" N MET A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 539 through 551 Processing helix chain 'A' and resid 553 through 562 removed outlier: 4.033A pdb=" N CYS A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 597 through 610 removed outlier: 4.199A pdb=" N TRP A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 605 " --> pdb=" O TRP A 601 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR A 606 " --> pdb=" O THR A 602 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 632 removed outlier: 3.685A pdb=" N ILE A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE A 628 " --> pdb=" O TRP A 624 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 657 Processing helix chain 'A' and resid 669 through 695 removed outlier: 3.571A pdb=" N MET A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 690 " --> pdb=" O PHE A 686 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 691 " --> pdb=" O MET A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.797A pdb=" N LYS B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 150 " --> pdb=" O CYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.648A pdb=" N GLY B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.617A pdb=" N ALA C 13 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 28 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 71 removed outlier: 3.621A pdb=" N LEU C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 99 removed outlier: 4.649A pdb=" N SER C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Proline residue: C 82 - end of helix Processing helix chain 'C' and resid 115 through 125 Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.667A pdb=" N ARG D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 101 removed outlier: 3.744A pdb=" N GLU D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'E' and resid 127 through 134 removed outlier: 3.738A pdb=" N ARG E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 173 removed outlier: 3.551A pdb=" N ILE E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 185 removed outlier: 3.706A pdb=" N TRP E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE E 183 " --> pdb=" O TRP E 179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 196 removed outlier: 3.741A pdb=" N LEU E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN E 194 " --> pdb=" O PHE E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 291 through 303 removed outlier: 4.031A pdb=" N LEU E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL E 301 " --> pdb=" O HIS E 297 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS E 303 " --> pdb=" O GLY E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 354 removed outlier: 3.771A pdb=" N GLU E 350 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 134 removed outlier: 3.639A pdb=" N ARG F 131 " --> pdb=" O SER F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 173 removed outlier: 3.552A pdb=" N ILE F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 185 removed outlier: 3.706A pdb=" N TRP F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE F 183 " --> pdb=" O TRP F 179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE F 185 " --> pdb=" O ARG F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 196 removed outlier: 4.055A pdb=" N ASN F 194 " --> pdb=" O PHE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 291 through 303 removed outlier: 4.032A pdb=" N LEU F 295 " --> pdb=" O PRO F 291 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET F 300 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL F 301 " --> pdb=" O HIS F 297 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 303 " --> pdb=" O GLY F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 354 removed outlier: 3.780A pdb=" N GLU F 350 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 134 removed outlier: 3.738A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 173 removed outlier: 3.689A pdb=" N VAL G 167 " --> pdb=" O TRP G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 185 removed outlier: 3.706A pdb=" N TRP G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG G 181 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE G 183 " --> pdb=" O TRP G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 196 removed outlier: 3.631A pdb=" N LEU G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN G 194 " --> pdb=" O PHE G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 291 through 303 removed outlier: 4.031A pdb=" N LEU G 295 " --> pdb=" O PRO G 291 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET G 300 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL G 301 " --> pdb=" O HIS G 297 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS G 303 " --> pdb=" O GLY G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 3.555A pdb=" N LYS G 354 " --> pdb=" O GLU G 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 134 removed outlier: 3.738A pdb=" N ARG H 131 " --> pdb=" O SER H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 173 removed outlier: 3.550A pdb=" N ILE H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 185 removed outlier: 3.706A pdb=" N TRP H 179 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG H 181 " --> pdb=" O ASN H 177 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE H 183 " --> pdb=" O TRP H 179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE H 185 " --> pdb=" O ARG H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 196 removed outlier: 3.741A pdb=" N LEU H 193 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN H 194 " --> pdb=" O PHE H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 238 Processing helix chain 'H' and resid 291 through 303 removed outlier: 4.031A pdb=" N LEU H 295 " --> pdb=" O PRO H 291 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET H 300 " --> pdb=" O VAL H 296 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL H 301 " --> pdb=" O HIS H 297 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS H 303 " --> pdb=" O GLY H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 354 removed outlier: 3.771A pdb=" N GLU H 350 " --> pdb=" O ALA H 346 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 134 removed outlier: 3.639A pdb=" N ARG I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 173 removed outlier: 3.552A pdb=" N ILE I 160 " --> pdb=" O ASN I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 185 removed outlier: 3.707A pdb=" N TRP I 179 " --> pdb=" O ALA I 175 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP I 182 " --> pdb=" O ASP I 178 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE I 183 " --> pdb=" O TRP I 179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE I 185 " --> pdb=" O ARG I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 196 removed outlier: 4.055A pdb=" N ASN I 194 " --> pdb=" O PHE I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 238 Processing helix chain 'I' and resid 291 through 303 removed outlier: 4.032A pdb=" N LEU I 295 " --> pdb=" O PRO I 291 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET I 300 " --> pdb=" O VAL I 296 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL I 301 " --> pdb=" O HIS I 297 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS I 303 " --> pdb=" O GLY I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 344 through 354 removed outlier: 3.780A pdb=" N GLU I 350 " --> pdb=" O ALA I 346 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS I 354 " --> pdb=" O GLU I 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 134 removed outlier: 3.737A pdb=" N ARG J 131 " --> pdb=" O SER J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 173 removed outlier: 3.690A pdb=" N VAL J 167 " --> pdb=" O TRP J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 185 removed outlier: 3.706A pdb=" N TRP J 179 " --> pdb=" O ALA J 175 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG J 181 " --> pdb=" O ASN J 177 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE J 183 " --> pdb=" O TRP J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 196 removed outlier: 3.631A pdb=" N LEU J 193 " --> pdb=" O ALA J 189 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN J 194 " --> pdb=" O PHE J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 238 Processing helix chain 'J' and resid 291 through 303 removed outlier: 4.030A pdb=" N LEU J 295 " --> pdb=" O PRO J 291 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET J 300 " --> pdb=" O VAL J 296 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL J 301 " --> pdb=" O HIS J 297 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS J 303 " --> pdb=" O GLY J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 354 removed outlier: 3.555A pdb=" N LYS J 354 " --> pdb=" O GLU J 350 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 64 removed outlier: 3.753A pdb=" N ILE a 64 " --> pdb=" O TRP a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 70 Processing helix chain 'a' and resid 71 through 91 removed outlier: 3.524A pdb=" N LEU a 82 " --> pdb=" O GLY a 78 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL a 85 " --> pdb=" O ALA a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 91 through 96 removed outlier: 3.518A pdb=" N ILE a 95 " --> pdb=" O GLY a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 116 removed outlier: 3.519A pdb=" N THR a 116 " --> pdb=" O TRP a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 117 through 124 Processing helix chain 'a' and resid 132 through 167 removed outlier: 3.691A pdb=" N ALA a 138 " --> pdb=" O ALA a 134 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA a 139 " --> pdb=" O ASP a 135 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY a 140 " --> pdb=" O LEU a 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA a 141 " --> pdb=" O GLU a 137 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS a 164 " --> pdb=" O GLY a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 187 through 194 Processing helix chain 'a' and resid 201 through 227 removed outlier: 4.656A pdb=" N GLY a 207 " --> pdb=" O LYS a 203 " (cutoff:3.500A) Proline residue: a 208 - end of helix Processing helix chain 'a' and resid 240 through 263 removed outlier: 3.565A pdb=" N ALA a 250 " --> pdb=" O SER a 246 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP a 261 " --> pdb=" O GLY a 257 " (cutoff:3.500A) Processing helix chain 'a' and resid 268 through 273 Processing helix chain 'a' and resid 274 through 301 removed outlier: 3.677A pdb=" N TYR a 288 " --> pdb=" O THR a 284 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 307 Processing helix chain 'a' and resid 310 through 316 Processing helix chain 'a' and resid 358 through 363 Processing helix chain 'a' and resid 363 through 401 removed outlier: 3.635A pdb=" N GLY a 380 " --> pdb=" O HIS a 376 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS a 397 " --> pdb=" O GLN a 393 " (cutoff:3.500A) Processing helix chain 'a' and resid 403 through 407 Processing helix chain 'a' and resid 409 through 414 Processing helix chain 'a' and resid 417 through 437 removed outlier: 3.581A pdb=" N LYS a 423 " --> pdb=" O GLU a 419 " (cutoff:3.500A) Processing helix chain 'a' and resid 437 through 452 removed outlier: 3.598A pdb=" N VAL a 442 " --> pdb=" O SER a 438 " (cutoff:3.500A) Processing helix chain 'a' and resid 471 through 475 Processing helix chain 'a' and resid 479 through 506 removed outlier: 3.539A pdb=" N MET a 485 " --> pdb=" O ASN a 481 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER a 496 " --> pdb=" O GLY a 492 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA a 499 " --> pdb=" O PHE a 495 " (cutoff:3.500A) Processing helix chain 'a' and resid 512 through 517 Processing helix chain 'a' and resid 530 through 534 Processing helix chain 'a' and resid 539 through 552 Processing helix chain 'a' and resid 553 through 563 removed outlier: 3.907A pdb=" N CYS a 559 " --> pdb=" O LEU a 555 " (cutoff:3.500A) Processing helix chain 'a' and resid 578 through 580 No H-bonds generated for 'chain 'a' and resid 578 through 580' Processing helix chain 'a' and resid 581 through 586 Processing helix chain 'a' and resid 597 through 610 removed outlier: 4.178A pdb=" N TRP a 601 " --> pdb=" O PHE a 597 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR a 604 " --> pdb=" O PHE a 600 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL a 605 " --> pdb=" O TRP a 601 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR a 606 " --> pdb=" O THR a 602 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE a 607 " --> pdb=" O GLU a 603 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER a 609 " --> pdb=" O VAL a 605 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER a 610 " --> pdb=" O THR a 606 " (cutoff:3.500A) Processing helix chain 'a' and resid 612 through 632 removed outlier: 3.679A pdb=" N ILE a 626 " --> pdb=" O LEU a 622 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER a 627 " --> pdb=" O VAL a 623 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE a 628 " --> pdb=" O TRP a 624 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA a 629 " --> pdb=" O PHE a 625 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL a 630 " --> pdb=" O ILE a 626 " (cutoff:3.500A) Processing helix chain 'a' and resid 634 through 657 Processing helix chain 'a' and resid 669 through 688 removed outlier: 3.703A pdb=" N LEU a 688 " --> pdb=" O GLY a 684 " (cutoff:3.500A) Processing helix chain 'a' and resid 688 through 695 Processing helix chain 'c' and resid 7 through 32 removed outlier: 3.571A pdb=" N ALA c 13 " --> pdb=" O LEU c 9 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE c 29 " --> pdb=" O PHE c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 71 removed outlier: 3.852A pdb=" N LEU c 46 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 99 removed outlier: 4.649A pdb=" N SER c 80 " --> pdb=" O LYS c 76 " (cutoff:3.500A) Proline residue: c 82 - end of helix removed outlier: 3.798A pdb=" N VAL c 91 " --> pdb=" O VAL c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 115 through 125 removed outlier: 3.927A pdb=" N ASN c 124 " --> pdb=" O LYS c 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 135 Processing sheet with id=AA2, first strand: chain 'B' and resid 157 through 161 Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 53 removed outlier: 7.266A pdb=" N GLU D 50 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU D 80 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER D 38 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 12.800A pdb=" N ILE D 75 " --> pdb=" O TYR D 121 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N TYR D 121 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE D 77 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 198 through 200 removed outlier: 6.950A pdb=" N ARG E 224 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL E 205 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 198 through 200 removed outlier: 5.725A pdb=" N THR E 112 " --> pdb=" O PRO E 153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE E 97 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 273 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR E 10 " --> pdb=" O ASN E 308 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASP E 310 " --> pdb=" O THR E 10 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA E 12 " --> pdb=" O ASP E 310 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLN E 312 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER E 14 " --> pdb=" O GLN E 312 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LYS E 314 " --> pdb=" O SER E 14 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR E 16 " --> pdb=" O LYS E 314 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL E 316 " --> pdb=" O TYR E 16 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE E 18 " --> pdb=" O VAL E 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.018A pdb=" N LEU E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 287 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE E 362 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU E 361 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA E 326 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU E 363 " --> pdb=" O ARG E 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 198 through 200 removed outlier: 6.931A pdb=" N ARG F 224 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL F 205 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 198 through 200 removed outlier: 5.726A pdb=" N THR F 112 " --> pdb=" O PRO F 153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE F 97 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE F 273 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR F 10 " --> pdb=" O ASN F 308 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASP F 310 " --> pdb=" O THR F 10 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA F 12 " --> pdb=" O ASP F 310 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLN F 312 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER F 14 " --> pdb=" O GLN F 312 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LYS F 314 " --> pdb=" O SER F 14 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR F 16 " --> pdb=" O LYS F 314 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL F 316 " --> pdb=" O TYR F 16 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE F 18 " --> pdb=" O VAL F 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 277 through 281 removed outlier: 6.017A pdb=" N LEU F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE F 287 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE F 362 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU F 361 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA F 326 " --> pdb=" O GLU F 361 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU F 363 " --> pdb=" O ARG F 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 198 through 200 removed outlier: 6.618A pdb=" N VAL G 218 " --> pdb=" O THR G 210 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N THR G 210 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL G 220 " --> pdb=" O LEU G 208 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU G 208 " --> pdb=" O VAL G 220 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG G 222 " --> pdb=" O ASN G 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 198 through 200 removed outlier: 5.249A pdb=" N THR G 112 " --> pdb=" O PRO G 153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE G 97 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG G 66 " --> pdb=" O LYS G 56 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE G 273 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA G 12 " --> pdb=" O ASP G 310 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLN G 312 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER G 14 " --> pdb=" O GLN G 312 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LYS G 314 " --> pdb=" O SER G 14 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR G 16 " --> pdb=" O LYS G 314 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL G 316 " --> pdb=" O TYR G 16 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE G 18 " --> pdb=" O VAL G 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 277 through 281 removed outlier: 6.018A pdb=" N LEU G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE G 287 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE G 362 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU G 361 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA G 326 " --> pdb=" O GLU G 361 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU G 363 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 198 through 200 removed outlier: 6.950A pdb=" N ARG H 224 " --> pdb=" O VAL H 205 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL H 205 " --> pdb=" O ARG H 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 198 through 200 removed outlier: 5.725A pdb=" N THR H 112 " --> pdb=" O PRO H 153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE H 97 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE H 273 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA H 12 " --> pdb=" O ASP H 310 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLN H 312 " --> pdb=" O ALA H 12 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER H 14 " --> pdb=" O GLN H 312 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LYS H 314 " --> pdb=" O SER H 14 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR H 16 " --> pdb=" O LYS H 314 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL H 316 " --> pdb=" O TYR H 16 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE H 18 " --> pdb=" O VAL H 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 277 through 281 removed outlier: 6.018A pdb=" N LEU H 284 " --> pdb=" O ALA H 280 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE H 287 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE H 362 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU H 361 " --> pdb=" O ALA H 326 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA H 326 " --> pdb=" O GLU H 361 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU H 363 " --> pdb=" O ARG H 324 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 198 through 200 removed outlier: 6.929A pdb=" N ARG I 224 " --> pdb=" O VAL I 205 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL I 205 " --> pdb=" O ARG I 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 198 through 200 removed outlier: 5.725A pdb=" N THR I 112 " --> pdb=" O PRO I 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE I 97 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE I 273 " --> pdb=" O GLY I 28 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR I 10 " --> pdb=" O ASN I 308 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP I 310 " --> pdb=" O THR I 10 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA I 12 " --> pdb=" O ASP I 310 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLN I 312 " --> pdb=" O ALA I 12 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER I 14 " --> pdb=" O GLN I 312 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LYS I 314 " --> pdb=" O SER I 14 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR I 16 " --> pdb=" O LYS I 314 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL I 316 " --> pdb=" O TYR I 16 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE I 18 " --> pdb=" O VAL I 316 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 277 through 281 removed outlier: 6.017A pdb=" N LEU I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE I 287 " --> pdb=" O ILE I 362 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE I 362 " --> pdb=" O ILE I 287 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU I 361 " --> pdb=" O ALA I 326 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA I 326 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU I 363 " --> pdb=" O ARG I 324 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 198 through 200 removed outlier: 6.618A pdb=" N VAL J 218 " --> pdb=" O THR J 210 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N THR J 210 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 220 " --> pdb=" O LEU J 208 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU J 208 " --> pdb=" O VAL J 220 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG J 222 " --> pdb=" O ASN J 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 198 through 200 removed outlier: 5.250A pdb=" N THR J 112 " --> pdb=" O PRO J 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE J 97 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG J 66 " --> pdb=" O PRO J 57 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N SER J 68 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL J 55 " --> pdb=" O SER J 68 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL J 70 " --> pdb=" O LEU J 53 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU J 53 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU J 72 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL J 51 " --> pdb=" O GLU J 72 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE J 74 " --> pdb=" O CYS J 49 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N CYS J 49 " --> pdb=" O ILE J 74 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE J 273 " --> pdb=" O GLY J 28 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA J 12 " --> pdb=" O ASP J 310 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLN J 312 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER J 14 " --> pdb=" O GLN J 312 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LYS J 314 " --> pdb=" O SER J 14 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR J 16 " --> pdb=" O LYS J 314 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL J 316 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE J 18 " --> pdb=" O VAL J 316 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 277 through 281 removed outlier: 6.017A pdb=" N LEU J 284 " --> pdb=" O ALA J 280 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE J 287 " --> pdb=" O ILE J 362 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE J 362 " --> pdb=" O ILE J 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 170 through 171 removed outlier: 3.904A pdb=" N ASN a 171 " --> pdb=" O ARG a 176 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG a 176 " --> pdb=" O ASN a 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'a' and resid 333 through 334 removed outlier: 3.984A pdb=" N VAL a 333 " --> pdb=" O ILE a 340 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE a 340 " --> pdb=" O VAL a 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 1717 hydrogen bonds defined for protein. 4806 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: 9.43 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.28: 5289 1.28 - 1.53: 26796 1.53 - 1.78: 5415 1.78 - 2.03: 257 2.03 - 2.28: 297 Bond restraints: 38054 Sorted by residual: bond pdb=" C40 F39 a 816 " pdb=" C41 F39 a 816 " ideal model delta sigma weight residual 1.352 1.618 -0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" C40 F39 A 816 " pdb=" C41 F39 A 816 " ideal model delta sigma weight residual 1.352 1.613 -0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C53 F39 a 816 " pdb=" C56 F39 a 816 " ideal model delta sigma weight residual 1.339 1.586 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C53 F39 A 816 " pdb=" C56 F39 A 816 " ideal model delta sigma weight residual 1.339 1.583 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" NA GS0 a 801 " pdb="MG GS0 a 801 " ideal model delta sigma weight residual 2.143 1.905 0.238 2.00e-02 2.50e+03 1.42e+02 ... (remaining 38049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 51378 4.05 - 8.11: 1196 8.11 - 12.16: 128 12.16 - 16.22: 38 16.22 - 20.27: 14 Bond angle restraints: 52754 Sorted by residual: angle pdb=" NB BCL A 815 " pdb="MG BCL A 815 " pdb=" ND BCL A 815 " ideal model delta sigma weight residual 157.70 174.83 -17.13 2.51e+00 1.58e-01 4.65e+01 angle pdb=" NB BCL a 815 " pdb="MG BCL a 815 " pdb=" ND BCL a 815 " ideal model delta sigma weight residual 157.70 174.80 -17.10 2.51e+00 1.58e-01 4.63e+01 angle pdb=" C62 F39 A 816 " pdb=" C64 F39 A 816 " pdb=" C63 F39 A 816 " ideal model delta sigma weight residual 130.94 110.67 20.27 3.00e+00 1.11e-01 4.57e+01 angle pdb=" N ARG c 104 " pdb=" CA ARG c 104 " pdb=" C ARG c 104 " ideal model delta sigma weight residual 110.20 99.83 10.37 1.58e+00 4.01e-01 4.31e+01 angle pdb=" C51 F39 a 816 " pdb=" C57 F39 a 816 " pdb=" C59 F39 a 816 " ideal model delta sigma weight residual 126.47 107.47 19.00 3.00e+00 1.11e-01 4.01e+01 ... (remaining 52749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 19985 35.99 - 71.97: 705 71.97 - 107.96: 60 107.96 - 143.95: 15 143.95 - 179.93: 15 Dihedral angle restraints: 20780 sinusoidal: 9552 harmonic: 11228 Sorted by residual: dihedral pdb=" CBD BCL I 402 " pdb=" CGD BCL I 402 " pdb=" O2D BCL I 402 " pdb=" CED BCL I 402 " ideal model delta sinusoidal sigma weight residual 180.00 49.77 130.23 1 5.00e+00 4.00e-02 6.32e+02 dihedral pdb=" CBD BCL F 402 " pdb=" CGD BCL F 402 " pdb=" O2D BCL F 402 " pdb=" CED BCL F 402 " ideal model delta sinusoidal sigma weight residual 180.00 49.86 130.14 1 5.00e+00 4.00e-02 6.32e+02 dihedral pdb=" C1 BCL G 405 " pdb=" C2 BCL G 405 " pdb=" C3 BCL G 405 " pdb=" C5 BCL G 405 " ideal model delta sinusoidal sigma weight residual -180.00 -0.07 -179.93 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 20777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3977 0.117 - 0.234: 1125 0.234 - 0.351: 140 0.351 - 0.467: 11 0.467 - 0.584: 5 Chirality restraints: 5258 Sorted by residual: chirality pdb=" C2CBBCL H 408 " pdb=" C1CBBCL H 408 " pdb=" C3CBBCL H 408 " pdb=" CMCBBCL H 408 " both_signs ideal model delta sigma weight residual False -2.62 -2.04 -0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" C2CBBCL E 408 " pdb=" C1CBBCL E 408 " pdb=" C3CBBCL E 408 " pdb=" CMCBBCL E 408 " both_signs ideal model delta sigma weight residual False -2.62 -2.04 -0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CBD BCL F 402 " pdb=" CAD BCL F 402 " pdb=" CGD BCL F 402 " pdb=" CHA BCL F 402 " both_signs ideal model delta sigma weight residual False 2.62 2.06 0.57 2.00e-01 2.50e+01 8.02e+00 ... (remaining 5255 not shown) Planarity restraints: 6529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C39 F39 a 816 " -0.175 2.00e-02 2.50e+03 3.38e-01 1.14e+03 pdb=" C40 F39 a 816 " 0.453 2.00e-02 2.50e+03 pdb=" C41 F39 a 816 " -0.441 2.00e-02 2.50e+03 pdb=" C42 F39 a 816 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 F39 a 816 " 0.069 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C20 F39 a 816 " -0.307 2.00e-02 2.50e+03 pdb=" C25 F39 a 816 " -0.032 2.00e-02 2.50e+03 pdb=" C27 F39 a 816 " 0.534 2.00e-02 2.50e+03 pdb=" C32 F39 a 816 " -0.265 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C56 F39 a 816 " -0.066 2.00e-02 2.50e+03 2.97e-01 1.11e+03 pdb=" C58 F39 a 816 " 0.305 2.00e-02 2.50e+03 pdb=" C60 F39 a 816 " 0.035 2.00e-02 2.50e+03 pdb=" C61 F39 a 816 " -0.528 2.00e-02 2.50e+03 pdb=" C63 F39 a 816 " 0.255 2.00e-02 2.50e+03 ... (remaining 6526 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 4 1.93 - 2.68: 964 2.68 - 3.42: 47567 3.42 - 4.16: 93861 4.16 - 4.90: 171103 Nonbonded interactions: 313499 Sorted by model distance: nonbonded pdb=" OE2 GLU A 55 " pdb=" CG PRO A 526 " model vdw 1.193 3.440 nonbonded pdb=" O ARG A 416 " pdb=" CZ3 TRP D 23 " model vdw 1.275 3.340 nonbonded pdb=" OE2 GLU a 450 " pdb=" O MET a 571 " model vdw 1.495 3.040 nonbonded pdb=" O ARG A 416 " pdb=" CH2 TRP D 23 " model vdw 1.548 3.340 nonbonded pdb=" CE1 HIS a 390 " pdb="MG BCL a 813 " model vdw 1.946 3.130 ... (remaining 313494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 820) selection = chain 'a' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = (chain 'E' and (resid 9 through 364 or resid 403 through 406)) selection = (chain 'F' and (resid 9 through 364 or resid 403 through 406)) selection = (chain 'G' and (resid 9 through 364 or resid 403 through 406)) selection = (chain 'H' and (resid 9 through 364 or resid 403 through 406)) selection = (chain 'I' and (resid 9 through 364 or resid 403 through 406)) selection = (chain 'J' and resid 9 through 404) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 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: 0.050 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 41.830 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 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 : 0.022 0.845 38194 Z= 1.826 Angle : 1.768 69.794 52790 Z= 0.992 Chirality : 0.103 0.584 5258 Planarity : 0.021 0.338 6529 Dihedral : 17.907 179.931 13628 Min Nonbonded Distance : 1.193 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -1.04 (0.13), residues: 3928 helix: -0.68 (0.15), residues: 1322 sheet: 0.25 (0.16), residues: 959 loop : -1.15 (0.13), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 43 TYR 0.045 0.002 TYR a 598 PHE 0.053 0.002 PHE B 218 TRP 0.044 0.002 TRP A 513 HIS 0.009 0.002 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.01370 / 0.85 (38054) covalent geometry : angle 1.64989 / 0.99 (52754) hydrogen bonds : bond 0.23032 / 15.37 ( 1705) hydrogen bonds : angle 9.37734 / 6.72 ( 4806) metal coordination : bond 0.12541 / 8.14 ( 12) metal coordination : angle 24.41122 / 13.34 ( 36) Misc. bond : bond 0.30566 / 19.27 ( 128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 720 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.7917 (pttt) cc_final: 0.7630 (ptmm) REVERT: A 509 THR cc_start: 0.7728 (p) cc_final: 0.7526 (p) REVERT: A 590 HIS cc_start: 0.6711 (m-70) cc_final: 0.6348 (m170) REVERT: C 99 TYR cc_start: 0.6267 (t80) cc_final: 0.5850 (t80) REVERT: F 322 LYS cc_start: 0.7888 (ptmt) cc_final: 0.7676 (pttp) REVERT: a 651 TRP cc_start: 0.6821 (t60) cc_final: 0.6049 (t60) outliers start: 0 outliers final: 4 residues processed: 720 average time/residue: 0.6490 time to fit residues: 571.8679 Evaluate side-chains 365 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 361 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 249 ASN Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 HIS D 133 ASN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN F 156 ASN F 157 ASN F 206 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 GLN H 194 ASN I 157 ASN I 305 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 ASN J 305 ASN ** J 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 ASN a 63 GLN a 266 ASN a 390 HIS a 418 GLN a 587 HIS c 39 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.212164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.169994 restraints weight = 38194.766| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 1.79 r_work: 0.4102 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.279 38194 Z= 0.183 Angle : 1.070 72.905 52790 Z= 0.376 Chirality : 0.046 0.177 5258 Planarity : 0.005 0.048 6529 Dihedral : 17.586 179.992 6547 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.17 % Favored : 98.80 % Rotamer: Outliers : 2.95 % Allowed : 12.08 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.28 (0.13), residues: 3928 helix: -0.00 (0.14), residues: 1428 sheet: 0.62 (0.16), residues: 1006 loop : -0.79 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 224 TYR 0.020 0.002 TYR A 599 PHE 0.031 0.002 PHE H 243 TRP 0.035 0.002 TRP D 23 HIS 0.011 0.002 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (38054) covalent geometry : angle 0.89157 / 0.37 (52754) hydrogen bonds : bond 0.04854 / 3.24 ( 1705) hydrogen bonds : angle 6.10304 / 4.31 ( 4806) metal coordination : bond 0.01313 / 0.90 ( 12) metal coordination : angle 22.63896 / 11.60 ( 36) Misc. bond : bond 0.06453 / 3.83 ( 128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 410 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6226 (ttp-170) cc_final: 0.5784 (mmp-170) REVERT: A 258 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7011 (mp) REVERT: A 311 LYS cc_start: 0.7634 (tmtt) cc_final: 0.7151 (tttt) REVERT: A 344 LYS cc_start: 0.7845 (pttt) cc_final: 0.7142 (ptmm) REVERT: A 419 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7387 (pp20) REVERT: A 532 TYR cc_start: 0.7055 (m-80) cc_final: 0.6670 (m-80) REVERT: A 570 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7587 (ttp) REVERT: A 603 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 640 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6469 (mt-10) REVERT: B 160 LYS cc_start: 0.7299 (ptmm) cc_final: 0.7041 (ptmt) REVERT: B 208 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6861 (t80) REVERT: C 99 TYR cc_start: 0.6347 (t80) cc_final: 0.5626 (t80) REVERT: E 255 GLU cc_start: 0.8369 (tt0) cc_final: 0.7951 (mp0) REVERT: E 268 LYS cc_start: 0.7880 (pttt) cc_final: 0.7367 (ttpp) REVERT: E 322 LYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5651 (pttt) REVERT: G 99 VAL cc_start: 0.7864 (t) cc_final: 0.7458 (p) REVERT: G 155 ASP cc_start: 0.7405 (m-30) cc_final: 0.7003 (t0) REVERT: G 193 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8064 (mm) REVERT: H 147 ASP cc_start: 0.5615 (OUTLIER) cc_final: 0.5202 (m-30) REVERT: H 211 GLU cc_start: 0.4063 (OUTLIER) cc_final: 0.3745 (tt0) REVERT: H 268 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6664 (mtmt) REVERT: H 285 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.4748 (tpm-80) REVERT: I 140 MET cc_start: 0.5032 (tpt) cc_final: 0.4821 (tpt) REVERT: I 292 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.5305 (tt) REVERT: I 329 GLN cc_start: 0.5823 (pm20) cc_final: 0.5419 (mp10) REVERT: J 64 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5397 (m-10) REVERT: J 156 ASN cc_start: 0.6797 (m-40) cc_final: 0.6241 (m110) REVERT: J 278 VAL cc_start: 0.8065 (m) cc_final: 0.7717 (p) REVERT: J 312 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.5801 (tm-30) outliers start: 97 outliers final: 42 residues processed: 469 average time/residue: 0.6153 time to fit residues: 354.4572 Evaluate side-chains 398 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 285 ARG Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 312 GLN Chi-restraints excluded: chain J residue 321 TYR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain a residue 654 LYS Chi-restraints excluded: chain c residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 247 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 317 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN E 156 ASN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 ASN I 80 ASN I 157 ASN J 133 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 GLN a 74 GLN a 263 ASN ** a 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.210824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.167663 restraints weight = 38061.099| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 1.71 r_work: 0.4108 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3992 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.302 38194 Z= 0.143 Angle : 0.990 73.970 52790 Z= 0.330 Chirality : 0.044 0.188 5258 Planarity : 0.004 0.039 6529 Dihedral : 16.517 179.988 6541 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.22 % Allowed : 14.24 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: 0.10 (0.13), residues: 3928 helix: 0.54 (0.14), residues: 1416 sheet: 0.65 (0.16), residues: 1005 loop : -0.69 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 224 TYR 0.025 0.002 TYR J 364 PHE 0.034 0.002 PHE E 243 TRP 0.039 0.001 TRP I 163 HIS 0.009 0.002 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (38054) covalent geometry : angle 0.80411 / 0.33 (52754) hydrogen bonds : bond 0.04075 / 2.72 ( 1705) hydrogen bonds : angle 5.44359 / 3.85 ( 4806) metal coordination : bond 0.01008 / 0.65 ( 12) metal coordination : angle 22.12869 / 11.04 ( 36) Misc. bond : bond 0.06486 / 3.93 ( 128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 367 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.7694 (p90) cc_final: 0.7491 (p90) REVERT: A 344 LYS cc_start: 0.7839 (pttt) cc_final: 0.7131 (ptmm) REVERT: A 414 LYS cc_start: 0.6918 (ttmt) cc_final: 0.6708 (mptp) REVERT: A 532 TYR cc_start: 0.7156 (m-80) cc_final: 0.6765 (m-80) REVERT: A 570 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7670 (ttp) REVERT: B 208 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6818 (t80) REVERT: C 99 TYR cc_start: 0.6445 (t80) cc_final: 0.5732 (t80) REVERT: D 66 MET cc_start: 0.6287 (ttp) cc_final: 0.6050 (tpp) REVERT: D 111 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5765 (ttpt) REVERT: D 134 LYS cc_start: 0.5053 (ttpt) cc_final: 0.4357 (ptpp) REVERT: D 136 TYR cc_start: 0.6848 (m-80) cc_final: 0.6633 (m-80) REVERT: E 66 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7194 (ttm-80) REVERT: E 255 GLU cc_start: 0.8160 (tt0) cc_final: 0.7904 (mp0) REVERT: E 261 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7535 (p0) REVERT: E 268 LYS cc_start: 0.7899 (pttt) cc_final: 0.7347 (ttpp) REVERT: E 322 LYS cc_start: 0.6018 (OUTLIER) cc_final: 0.5743 (pttt) REVERT: F 140 MET cc_start: 0.7759 (mmm) cc_final: 0.7386 (tpt) REVERT: G 155 ASP cc_start: 0.7408 (m-30) cc_final: 0.7136 (t0) REVERT: G 193 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8117 (mm) REVERT: H 195 GLU cc_start: 0.5764 (mm-30) cc_final: 0.5278 (tm-30) REVERT: H 211 GLU cc_start: 0.4127 (OUTLIER) cc_final: 0.3691 (tt0) REVERT: H 268 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6682 (mtmt) REVERT: I 140 MET cc_start: 0.5358 (tpt) cc_final: 0.5077 (tpt) REVERT: I 329 GLN cc_start: 0.5745 (pm20) cc_final: 0.5423 (mp10) REVERT: J 73 SER cc_start: 0.7885 (t) cc_final: 0.7602 (t) REVERT: J 158 ASP cc_start: 0.5928 (OUTLIER) cc_final: 0.4800 (m-30) REVERT: J 278 VAL cc_start: 0.8129 (m) cc_final: 0.7723 (p) REVERT: J 312 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.5929 (tm130) REVERT: a 651 TRP cc_start: 0.7235 (OUTLIER) cc_final: 0.6717 (t60) outliers start: 106 outliers final: 39 residues processed: 435 average time/residue: 0.6389 time to fit residues: 342.5392 Evaluate side-chains 367 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 316 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 337 GLU Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 312 GLN Chi-restraints excluded: chain J residue 321 TYR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain a residue 651 TRP Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 3 optimal weight: 0.7980 chunk 274 optimal weight: 9.9990 chunk 387 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 226 optimal weight: 30.0000 chunk 173 optimal weight: 8.9990 chunk 257 optimal weight: 8.9990 chunk 263 optimal weight: 20.0000 chunk 361 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 ASN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 HIS I 157 ASN J 90 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 ASN a 418 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.202456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.159892 restraints weight = 38196.328| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.71 r_work: 0.3996 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3887 r_free = 0.3887 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.317 38194 Z= 0.253 Angle : 1.143 79.368 52790 Z= 0.396 Chirality : 0.050 0.240 5258 Planarity : 0.006 0.058 6529 Dihedral : 16.679 179.939 6539 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.74 % Allowed : 15.88 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.41 (0.13), residues: 3928 helix: 0.06 (0.13), residues: 1400 sheet: 0.43 (0.15), residues: 1007 loop : -0.95 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 41 TYR 0.035 0.003 TYR a 202 PHE 0.032 0.002 PHE E 243 TRP 0.030 0.002 TRP I 163 HIS 0.015 0.003 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.25 (38054) covalent geometry : angle 0.95873 / 0.39 (52754) hydrogen bonds : bond 0.04732 / 3.14 ( 1705) hydrogen bonds : angle 5.51131 / 3.89 ( 4806) metal coordination : bond 0.02477 / 1.71 ( 12) metal coordination : angle 23.83835 / 12.36 ( 36) Misc. bond : bond 0.07019 / 4.64 ( 128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 348 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TYR cc_start: 0.6467 (t80) cc_final: 0.6217 (t80) REVERT: A 344 LYS cc_start: 0.7882 (pttt) cc_final: 0.7287 (pttp) REVERT: A 570 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7672 (ttp) REVERT: A 590 HIS cc_start: 0.7681 (m-70) cc_final: 0.7138 (m170) REVERT: B 131 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7778 (mtpp) REVERT: C 76 LYS cc_start: 0.6135 (tmtt) cc_final: 0.5502 (ttmt) REVERT: C 99 TYR cc_start: 0.6370 (t80) cc_final: 0.5712 (t80) REVERT: D 111 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.6035 (mtpt) REVERT: D 134 LYS cc_start: 0.5286 (ttpt) cc_final: 0.4681 (ptpp) REVERT: D 136 TYR cc_start: 0.6951 (m-80) cc_final: 0.6750 (m-80) REVERT: F 222 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7542 (ttp-170) REVERT: G 155 ASP cc_start: 0.7505 (m-30) cc_final: 0.7052 (t0) REVERT: H 195 GLU cc_start: 0.5872 (mm-30) cc_final: 0.5308 (tm-30) REVERT: H 211 GLU cc_start: 0.4299 (OUTLIER) cc_final: 0.3671 (tt0) REVERT: H 268 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6744 (mtmt) REVERT: H 335 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5631 (tm) REVERT: I 140 MET cc_start: 0.5906 (tpt) cc_final: 0.5666 (tpt) REVERT: I 232 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7107 (tpp) REVERT: I 255 GLU cc_start: 0.5036 (mt-10) cc_final: 0.4671 (tm-30) REVERT: I 292 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5529 (tt) REVERT: J 73 SER cc_start: 0.7925 (t) cc_final: 0.7613 (t) REVERT: J 278 VAL cc_start: 0.8167 (m) cc_final: 0.7829 (p) REVERT: J 339 ARG cc_start: 0.6694 (mtt-85) cc_final: 0.6469 (mtt90) REVERT: a 60 LYS cc_start: 0.7017 (mttp) cc_final: 0.5727 (mmmt) REVERT: a 73 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6766 (tp30) REVERT: a 200 LYS cc_start: 0.7123 (ptmt) cc_final: 0.6904 (pttm) REVERT: a 453 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6868 (mp) REVERT: a 651 TRP cc_start: 0.7299 (OUTLIER) cc_final: 0.6934 (t60) REVERT: a 654 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6496 (mtpt) REVERT: c 90 MET cc_start: 0.4032 (tmm) cc_final: 0.3601 (tmt) outliers start: 123 outliers final: 55 residues processed: 425 average time/residue: 0.6292 time to fit residues: 330.0176 Evaluate side-chains 366 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 298 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain I residue 11 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 321 TYR Chi-restraints excluded: chain a residue 73 GLU Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain a residue 453 ILE Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 651 TRP Chi-restraints excluded: chain a residue 654 LYS Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 4 optimal weight: 5.9990 chunk 182 optimal weight: 0.2980 chunk 303 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 338 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 297 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 ASN I 157 ASN I 306 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.205070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.162788 restraints weight = 38047.679| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.82 r_work: 0.4028 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.245 38194 Z= 0.151 Angle : 1.013 76.181 52790 Z= 0.332 Chirality : 0.044 0.160 5258 Planarity : 0.004 0.056 6529 Dihedral : 16.154 179.991 6539 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.38 % Allowed : 17.37 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 3928 helix: 0.42 (0.14), residues: 1415 sheet: 0.36 (0.15), residues: 1034 loop : -0.81 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 331 TYR 0.027 0.002 TYR c 112 PHE 0.036 0.002 PHE E 243 TRP 0.018 0.001 TRP c 52 HIS 0.010 0.002 HIS H 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (38054) covalent geometry : angle 0.81704 / 0.33 (52754) hydrogen bonds : bond 0.03903 / 2.61 ( 1705) hydrogen bonds : angle 5.17748 / 3.67 ( 4806) metal coordination : bond 0.01157 / 0.77 ( 12) metal coordination : angle 22.96630 / 11.75 ( 36) Misc. bond : bond 0.05920 / 3.92 ( 128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 316 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.7853 (pttt) cc_final: 0.7265 (pttp) REVERT: A 471 PHE cc_start: 0.7967 (m-80) cc_final: 0.7557 (m-80) REVERT: A 570 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7561 (ttp) REVERT: A 590 HIS cc_start: 0.7686 (m-70) cc_final: 0.7139 (m170) REVERT: B 131 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7798 (mtpp) REVERT: B 135 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7429 (mm) REVERT: C 76 LYS cc_start: 0.6134 (tmtt) cc_final: 0.5555 (ttmt) REVERT: D 111 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5948 (mtpt) REVERT: D 134 LYS cc_start: 0.5271 (ttpt) cc_final: 0.4662 (ptpp) REVERT: D 136 TYR cc_start: 0.6802 (m-80) cc_final: 0.6600 (m-80) REVERT: E 97 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7542 (pp) REVERT: E 140 MET cc_start: 0.6764 (mtp) cc_final: 0.6113 (mpm) REVERT: F 140 MET cc_start: 0.7947 (mmm) cc_final: 0.7511 (tpt) REVERT: F 222 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7439 (ttp-170) REVERT: G 112 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7539 (m) REVERT: G 155 ASP cc_start: 0.7531 (m-30) cc_final: 0.7038 (t0) REVERT: H 195 GLU cc_start: 0.5795 (mm-30) cc_final: 0.5281 (tm-30) REVERT: H 211 GLU cc_start: 0.4475 (OUTLIER) cc_final: 0.3745 (tt0) REVERT: H 246 ASP cc_start: 0.6506 (p0) cc_final: 0.6037 (m-30) REVERT: H 268 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6699 (mtmt) REVERT: H 335 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5648 (tt) REVERT: I 140 MET cc_start: 0.6018 (tpt) cc_final: 0.5750 (tpt) REVERT: I 150 MET cc_start: 0.7140 (mtp) cc_final: 0.6726 (mtm) REVERT: I 211 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6298 (pp20) REVERT: I 255 GLU cc_start: 0.4880 (mt-10) cc_final: 0.4573 (tm-30) REVERT: I 292 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.5387 (tt) REVERT: J 73 SER cc_start: 0.7901 (t) cc_final: 0.7593 (t) REVERT: J 278 VAL cc_start: 0.8169 (m) cc_final: 0.7822 (p) REVERT: J 312 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: J 339 ARG cc_start: 0.6635 (mtt-85) cc_final: 0.6414 (mtt90) REVERT: a 60 LYS cc_start: 0.6983 (mttp) cc_final: 0.5710 (mmpt) REVERT: a 453 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6680 (mp) REVERT: a 651 TRP cc_start: 0.7247 (OUTLIER) cc_final: 0.6832 (t60) REVERT: c 90 MET cc_start: 0.4191 (tmm) cc_final: 0.3703 (tmt) outliers start: 111 outliers final: 49 residues processed: 389 average time/residue: 0.5834 time to fit residues: 283.0860 Evaluate side-chains 346 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 282 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 80 ASN Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 337 GLU Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 312 GLN Chi-restraints excluded: chain J residue 321 TYR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain a residue 453 ILE Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 651 TRP Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 356 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 18 optimal weight: 0.0980 chunk 364 optimal weight: 4.9990 chunk 365 optimal weight: 5.9990 chunk 238 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 133 ASN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 418 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.203067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.160542 restraints weight = 38115.019| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.77 r_work: 0.3986 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.268 38194 Z= 0.198 Angle : 1.064 78.523 52790 Z= 0.356 Chirality : 0.046 0.202 5258 Planarity : 0.005 0.055 6529 Dihedral : 16.128 179.988 6539 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.32 % Allowed : 18.19 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.27 (0.13), residues: 3928 helix: 0.41 (0.14), residues: 1388 sheet: 0.33 (0.16), residues: 1034 loop : -1.00 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 331 TYR 0.028 0.002 TYR H 345 PHE 0.031 0.002 PHE a 692 TRP 0.047 0.002 TRP I 239 HIS 0.011 0.002 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (38054) covalent geometry : angle 0.87256 / 0.35 (52754) hydrogen bonds : bond 0.04199 / 2.79 ( 1705) hydrogen bonds : angle 5.18120 / 3.66 ( 4806) metal coordination : bond 0.01812 / 1.24 ( 12) metal coordination : angle 23.31459 / 11.92 ( 36) Misc. bond : bond 0.06085 / 3.99 ( 128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 321 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.7888 (pttt) cc_final: 0.7288 (pttp) REVERT: A 570 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7558 (ttp) REVERT: A 590 HIS cc_start: 0.7779 (m-70) cc_final: 0.7252 (m170) REVERT: B 135 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7410 (mm) REVERT: B 214 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: B 228 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5580 (ttp-110) REVERT: C 76 LYS cc_start: 0.6119 (tmtt) cc_final: 0.5559 (ttmt) REVERT: C 92 MET cc_start: 0.5792 (mtm) cc_final: 0.3671 (ptm) REVERT: D 111 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5972 (mtpt) REVERT: D 134 LYS cc_start: 0.5308 (ttpt) cc_final: 0.4686 (ptpp) REVERT: D 136 TYR cc_start: 0.6839 (m-80) cc_final: 0.6600 (m-80) REVERT: E 97 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7552 (pp) REVERT: E 191 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7709 (p) REVERT: F 140 MET cc_start: 0.7990 (mmm) cc_final: 0.7565 (tpt) REVERT: F 222 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7518 (ttp-170) REVERT: G 112 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7735 (m) REVERT: H 112 THR cc_start: 0.7080 (OUTLIER) cc_final: 0.6763 (t) REVERT: H 195 GLU cc_start: 0.5851 (mm-30) cc_final: 0.5310 (tm-30) REVERT: H 211 GLU cc_start: 0.4333 (OUTLIER) cc_final: 0.3657 (tt0) REVERT: H 246 ASP cc_start: 0.6551 (p0) cc_final: 0.6029 (m-30) REVERT: H 268 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6738 (mtmt) REVERT: H 314 LYS cc_start: 0.7661 (tttt) cc_final: 0.6754 (tppp) REVERT: H 335 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5540 (tt) REVERT: I 13 HIS cc_start: 0.6739 (m-70) cc_final: 0.6416 (m-70) REVERT: I 140 MET cc_start: 0.6101 (tpt) cc_final: 0.5841 (tpt) REVERT: I 255 GLU cc_start: 0.4838 (mt-10) cc_final: 0.4554 (tm-30) REVERT: I 292 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5479 (tt) REVERT: J 73 SER cc_start: 0.7912 (t) cc_final: 0.7613 (t) REVERT: J 278 VAL cc_start: 0.8194 (m) cc_final: 0.7864 (p) REVERT: J 312 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6518 (tm-30) REVERT: J 339 ARG cc_start: 0.6720 (mtt-85) cc_final: 0.6506 (mtt90) REVERT: a 60 LYS cc_start: 0.6946 (mttp) cc_final: 0.5341 (tptp) REVERT: a 453 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6841 (mp) REVERT: a 651 TRP cc_start: 0.7296 (OUTLIER) cc_final: 0.6883 (t60) REVERT: c 90 MET cc_start: 0.4144 (tmm) cc_final: 0.3676 (tmt) REVERT: c 94 LEU cc_start: 0.3536 (tp) cc_final: 0.3091 (tt) outliers start: 109 outliers final: 63 residues processed: 399 average time/residue: 0.5937 time to fit residues: 297.2507 Evaluate side-chains 374 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 294 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain I residue 11 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 80 ASN Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 337 GLU Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 312 GLN Chi-restraints excluded: chain J residue 321 TYR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain a residue 397 LYS Chi-restraints excluded: chain a residue 453 ILE Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 651 TRP Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 323 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.203334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.161973 restraints weight = 38286.879| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 1.83 r_work: 0.4004 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.250 38194 Z= 0.182 Angle : 1.040 78.082 52790 Z= 0.345 Chirality : 0.045 0.187 5258 Planarity : 0.005 0.055 6529 Dihedral : 16.045 179.995 6539 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.41 % Allowed : 18.95 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.23 (0.13), residues: 3928 helix: 0.48 (0.14), residues: 1383 sheet: 0.33 (0.16), residues: 1034 loop : -1.01 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 224 TYR 0.031 0.002 TYR A 114 PHE 0.044 0.002 PHE E 243 TRP 0.039 0.002 TRP I 239 HIS 0.010 0.002 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (38054) covalent geometry : angle 0.84728 / 0.34 (52754) hydrogen bonds : bond 0.04049 / 2.70 ( 1705) hydrogen bonds : angle 5.13895 / 3.63 ( 4806) metal coordination : bond 0.01590 / 1.09 ( 12) metal coordination : angle 23.09909 / 11.74 ( 36) Misc. bond : bond 0.05878 / 3.87 ( 128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 302 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7474 (tttm) REVERT: A 222 ILE cc_start: 0.6577 (OUTLIER) cc_final: 0.6149 (mp) REVERT: A 344 LYS cc_start: 0.7868 (pttt) cc_final: 0.7256 (pttp) REVERT: A 570 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7561 (ttp) REVERT: A 590 HIS cc_start: 0.7783 (m-70) cc_final: 0.7251 (m170) REVERT: B 135 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7269 (mm) REVERT: B 137 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: B 214 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: B 228 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5484 (ttp-110) REVERT: C 76 LYS cc_start: 0.6051 (tmtt) cc_final: 0.5503 (ttmt) REVERT: C 92 MET cc_start: 0.5744 (mtm) cc_final: 0.3676 (ptm) REVERT: D 134 LYS cc_start: 0.5366 (ttpt) cc_final: 0.4767 (ptpp) REVERT: D 136 TYR cc_start: 0.6773 (m-80) cc_final: 0.6519 (m-80) REVERT: E 97 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7488 (pp) REVERT: E 191 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7669 (p) REVERT: F 140 MET cc_start: 0.7973 (mmm) cc_final: 0.7542 (tpt) REVERT: F 222 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7502 (ttp-170) REVERT: F 253 GLN cc_start: 0.7512 (pt0) cc_final: 0.7268 (pt0) REVERT: G 112 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7729 (m) REVERT: H 112 THR cc_start: 0.6990 (OUTLIER) cc_final: 0.6699 (t) REVERT: H 128 ASP cc_start: 0.5994 (t0) cc_final: 0.5650 (t0) REVERT: H 150 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6771 (mtp) REVERT: H 195 GLU cc_start: 0.5804 (mm-30) cc_final: 0.5278 (tm-30) REVERT: H 211 GLU cc_start: 0.4351 (OUTLIER) cc_final: 0.3722 (tt0) REVERT: H 268 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6785 (mtmt) REVERT: H 314 LYS cc_start: 0.7692 (tttt) cc_final: 0.6791 (tppp) REVERT: H 335 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5568 (tt) REVERT: I 13 HIS cc_start: 0.6853 (m-70) cc_final: 0.6545 (m-70) REVERT: I 140 MET cc_start: 0.6118 (tpt) cc_final: 0.5832 (tpt) REVERT: I 150 MET cc_start: 0.6844 (mtp) cc_final: 0.6440 (mtm) REVERT: I 255 GLU cc_start: 0.4779 (mt-10) cc_final: 0.4470 (tm-30) REVERT: I 292 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5420 (tt) REVERT: J 73 SER cc_start: 0.7975 (t) cc_final: 0.7673 (t) REVERT: J 116 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7556 (tm-30) REVERT: J 151 LYS cc_start: 0.6872 (tttt) cc_final: 0.6600 (ttpt) REVERT: J 278 VAL cc_start: 0.8169 (m) cc_final: 0.7828 (p) REVERT: J 312 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6447 (tm-30) REVERT: J 339 ARG cc_start: 0.6635 (mtt-85) cc_final: 0.6420 (mtt90) REVERT: a 60 LYS cc_start: 0.6927 (mttp) cc_final: 0.5633 (mmmt) REVERT: a 453 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6804 (mp) REVERT: a 651 TRP cc_start: 0.7269 (OUTLIER) cc_final: 0.6865 (t60) REVERT: c 90 MET cc_start: 0.4250 (tmm) cc_final: 0.3738 (tmt) REVERT: c 94 LEU cc_start: 0.3599 (tp) cc_final: 0.3140 (tt) outliers start: 112 outliers final: 65 residues processed: 379 average time/residue: 0.5688 time to fit residues: 269.7769 Evaluate side-chains 372 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 288 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain I residue 11 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 80 ASN Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 249 ASN Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 337 GLU Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 312 GLN Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain a residue 274 ASP Chi-restraints excluded: chain a residue 397 LYS Chi-restraints excluded: chain a residue 453 ILE Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 651 TRP Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 174 optimal weight: 0.0870 chunk 219 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 341 optimal weight: 0.9980 chunk 317 optimal weight: 3.9990 chunk 328 optimal weight: 0.5980 chunk 267 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 1.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 GLN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.205159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.163221 restraints weight = 37996.944| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 1.81 r_work: 0.4033 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 38194 Z= 0.145 Angle : 0.992 76.826 52790 Z= 0.323 Chirality : 0.043 0.163 5258 Planarity : 0.004 0.055 6529 Dihedral : 15.792 179.994 6539 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.83 % Allowed : 19.71 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.06 (0.13), residues: 3928 helix: 0.63 (0.14), residues: 1414 sheet: 0.35 (0.16), residues: 1036 loop : -0.89 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 224 TYR 0.032 0.002 TYR H 345 PHE 0.033 0.002 PHE E 243 TRP 0.041 0.002 TRP I 239 HIS 0.009 0.002 HIS H 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (38054) covalent geometry : angle 0.79850 / 0.32 (52754) hydrogen bonds : bond 0.03727 / 2.48 ( 1705) hydrogen bonds : angle 4.97822 / 3.53 ( 4806) metal coordination : bond 0.01090 / 0.73 ( 12) metal coordination : angle 22.57971 / 11.34 ( 36) Misc. bond : bond 0.05620 / 3.70 ( 128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 303 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7478 (tttm) REVERT: A 222 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6216 (mp) REVERT: A 344 LYS cc_start: 0.7855 (pttt) cc_final: 0.7224 (pttp) REVERT: A 590 HIS cc_start: 0.7751 (m-70) cc_final: 0.7222 (m170) REVERT: B 135 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7457 (mm) REVERT: B 137 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: B 228 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.5521 (ttp-110) REVERT: C 26 SER cc_start: 0.6065 (m) cc_final: 0.5847 (m) REVERT: C 76 LYS cc_start: 0.6019 (tmtt) cc_final: 0.5478 (ttmt) REVERT: C 92 MET cc_start: 0.5736 (mtm) cc_final: 0.3713 (ptm) REVERT: D 68 ARG cc_start: 0.6696 (tmm160) cc_final: 0.6452 (ttp80) REVERT: D 134 LYS cc_start: 0.5386 (ttpt) cc_final: 0.4832 (ptpp) REVERT: E 97 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7466 (pp) REVERT: E 191 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7625 (p) REVERT: F 140 MET cc_start: 0.7998 (mmm) cc_final: 0.7552 (tpt) REVERT: F 222 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7447 (ttp-170) REVERT: F 253 GLN cc_start: 0.7440 (pt0) cc_final: 0.7180 (pt0) REVERT: G 112 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7761 (m) REVERT: H 112 THR cc_start: 0.6953 (OUTLIER) cc_final: 0.6676 (t) REVERT: H 128 ASP cc_start: 0.5944 (t0) cc_final: 0.5601 (t0) REVERT: H 195 GLU cc_start: 0.5823 (mm-30) cc_final: 0.5362 (tm-30) REVERT: H 268 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6791 (mtmt) REVERT: H 300 MET cc_start: 0.7559 (mtp) cc_final: 0.7215 (mtp) REVERT: H 335 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5712 (tt) REVERT: I 13 HIS cc_start: 0.6915 (m-70) cc_final: 0.6539 (m-70) REVERT: I 140 MET cc_start: 0.6147 (tpt) cc_final: 0.5863 (tpt) REVERT: I 150 MET cc_start: 0.6782 (mtp) cc_final: 0.6341 (mtm) REVERT: I 255 GLU cc_start: 0.4772 (mt-10) cc_final: 0.4418 (tm-30) REVERT: I 270 ASP cc_start: 0.5200 (p0) cc_final: 0.4763 (p0) REVERT: I 292 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5471 (tt) REVERT: I 310 ASP cc_start: 0.6957 (t0) cc_final: 0.6611 (t0) REVERT: J 73 SER cc_start: 0.7988 (t) cc_final: 0.7680 (t) REVERT: J 116 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7528 (tm-30) REVERT: J 151 LYS cc_start: 0.6909 (tttt) cc_final: 0.6674 (ttpt) REVERT: J 278 VAL cc_start: 0.8159 (m) cc_final: 0.7813 (p) REVERT: J 312 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: J 339 ARG cc_start: 0.6581 (mtt-85) cc_final: 0.6370 (mtt90) REVERT: a 60 LYS cc_start: 0.6941 (mttp) cc_final: 0.5668 (mmmt) REVERT: a 130 SER cc_start: 0.7337 (OUTLIER) cc_final: 0.7120 (p) REVERT: a 453 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6759 (mp) REVERT: a 651 TRP cc_start: 0.7283 (OUTLIER) cc_final: 0.6876 (t60) REVERT: c 90 MET cc_start: 0.4279 (tmm) cc_final: 0.3753 (tmt) REVERT: c 94 LEU cc_start: 0.3650 (tp) cc_final: 0.3197 (tt) outliers start: 93 outliers final: 52 residues processed: 370 average time/residue: 0.6119 time to fit residues: 282.7290 Evaluate side-chains 347 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 279 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 78 PHE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 249 ASN Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 337 GLU Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 312 GLN Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 453 ILE Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 651 TRP Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 83 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 371 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 330 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 ASN D 48 GLN E 305 ASN F 157 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 ASN ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 418 GLN a 587 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.198237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.156018 restraints weight = 38598.191| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.89 r_work: 0.3922 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.323 38194 Z= 0.364 Angle : 1.262 80.629 52790 Z= 0.448 Chirality : 0.056 0.308 5258 Planarity : 0.006 0.063 6529 Dihedral : 16.726 179.964 6539 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.50 % Allowed : 19.38 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.90 (0.13), residues: 3928 helix: -0.30 (0.13), residues: 1384 sheet: 0.19 (0.15), residues: 1040 loop : -1.34 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 250 TYR 0.048 0.003 TYR A 114 PHE 0.039 0.003 PHE a 692 TRP 0.041 0.003 TRP I 239 HIS 0.018 0.003 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00904 / 0.36 (38054) covalent geometry : angle 1.09205 / 0.44 (52754) hydrogen bonds : bond 0.05259 / 3.46 ( 1705) hydrogen bonds : angle 5.55031 / 3.91 ( 4806) metal coordination : bond 0.03394 / 2.43 ( 12) metal coordination : angle 24.27137 / 12.59 ( 36) Misc. bond : bond 0.07434 / 4.83 ( 128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 298 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7919 (ptpt) cc_final: 0.7548 (tttm) REVERT: A 344 LYS cc_start: 0.7890 (pttt) cc_final: 0.7230 (pttp) REVERT: A 590 HIS cc_start: 0.7873 (m-70) cc_final: 0.7671 (m-70) REVERT: A 597 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: B 135 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7544 (mm) REVERT: B 137 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: B 228 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5438 (mtp-110) REVERT: C 76 LYS cc_start: 0.6095 (tmtt) cc_final: 0.5584 (ttmt) REVERT: D 134 LYS cc_start: 0.5501 (ttpt) cc_final: 0.4882 (ptpp) REVERT: D 136 TYR cc_start: 0.6991 (m-80) cc_final: 0.6533 (m-10) REVERT: E 97 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7554 (pp) REVERT: F 54 ASN cc_start: 0.6892 (m110) cc_final: 0.6048 (t0) REVERT: F 222 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7566 (ttp-170) REVERT: F 253 GLN cc_start: 0.7565 (pt0) cc_final: 0.7328 (pt0) REVERT: G 112 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8002 (m) REVERT: G 140 MET cc_start: 0.7355 (tpp) cc_final: 0.7105 (tpt) REVERT: H 112 THR cc_start: 0.7074 (OUTLIER) cc_final: 0.6737 (t) REVERT: H 128 ASP cc_start: 0.5940 (t0) cc_final: 0.5614 (t0) REVERT: H 195 GLU cc_start: 0.5891 (mm-30) cc_final: 0.5498 (mm-30) REVERT: H 268 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7008 (mtmt) REVERT: I 13 HIS cc_start: 0.7006 (m-70) cc_final: 0.6621 (m-70) REVERT: I 140 MET cc_start: 0.6249 (tpt) cc_final: 0.5972 (tpt) REVERT: I 255 GLU cc_start: 0.4798 (mt-10) cc_final: 0.4400 (tm-30) REVERT: I 292 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.5769 (tt) REVERT: I 310 ASP cc_start: 0.7144 (t0) cc_final: 0.6727 (t0) REVERT: J 64 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5270 (m-80) REVERT: J 73 SER cc_start: 0.7975 (t) cc_final: 0.7714 (t) REVERT: J 116 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7627 (tm-30) REVERT: J 151 LYS cc_start: 0.7002 (tttt) cc_final: 0.6711 (ttpt) REVERT: J 312 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: a 60 LYS cc_start: 0.7062 (mttp) cc_final: 0.5784 (mmmt) REVERT: a 453 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.6927 (mp) REVERT: a 651 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.6934 (t60) REVERT: c 90 MET cc_start: 0.4270 (tmm) cc_final: 0.3745 (tmt) REVERT: c 94 LEU cc_start: 0.3840 (tp) cc_final: 0.3404 (tt) outliers start: 115 outliers final: 65 residues processed: 380 average time/residue: 0.6240 time to fit residues: 295.7593 Evaluate side-chains 365 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 286 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain I residue 11 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 221 SER Chi-restraints excluded: chain I residue 249 ASN Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 337 GLU Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 310 ASP Chi-restraints excluded: chain J residue 312 GLN Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain a residue 355 LEU Chi-restraints excluded: chain a residue 397 LYS Chi-restraints excluded: chain a residue 453 ILE Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 604 THR Chi-restraints excluded: chain a residue 651 TRP Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 59 optimal weight: 0.8980 chunk 341 optimal weight: 1.9990 chunk 323 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 chunk 361 optimal weight: 0.6980 chunk 337 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 GLN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 305 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 ASN J 312 GLN a 508 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.203915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.162008 restraints weight = 38114.064| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 1.80 r_work: 0.4017 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (14 function evaluations) r_final: 0.3905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 38194 Z= 0.151 Angle : 1.026 77.228 52790 Z= 0.340 Chirality : 0.044 0.166 5258 Planarity : 0.004 0.065 6529 Dihedral : 16.033 179.942 6539 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.34 % Allowed : 20.69 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.31 (0.13), residues: 3928 helix: 0.38 (0.14), residues: 1402 sheet: 0.36 (0.16), residues: 1000 loop : -1.05 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 224 TYR 0.037 0.002 TYR H 345 PHE 0.053 0.002 PHE E 243 TRP 0.048 0.002 TRP I 239 HIS 0.010 0.002 HIS H 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (38054) covalent geometry : angle 0.83386 / 0.34 (52754) hydrogen bonds : bond 0.03875 / 2.59 ( 1705) hydrogen bonds : angle 5.08912 / 3.59 ( 4806) metal coordination : bond 0.01141 / 0.74 ( 12) metal coordination : angle 22.88640 / 11.62 ( 36) Misc. bond : bond 0.05445 / 3.65 ( 128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 308 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7788 (ptpt) cc_final: 0.7473 (tttm) REVERT: A 344 LYS cc_start: 0.7852 (pttt) cc_final: 0.7144 (ptmm) REVERT: A 590 HIS cc_start: 0.7791 (m-70) cc_final: 0.7454 (m170) REVERT: B 135 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7454 (mm) REVERT: B 137 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: B 228 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5476 (ttp-110) REVERT: C 76 LYS cc_start: 0.6109 (tmtt) cc_final: 0.5630 (ttmt) REVERT: C 92 MET cc_start: 0.5769 (mtm) cc_final: 0.3561 (ptm) REVERT: D 134 LYS cc_start: 0.5420 (ttpt) cc_final: 0.4831 (ptpp) REVERT: E 97 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7488 (pp) REVERT: F 140 MET cc_start: 0.7990 (mmm) cc_final: 0.7542 (tpt) REVERT: F 222 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7422 (ttp-170) REVERT: F 253 GLN cc_start: 0.7517 (pt0) cc_final: 0.7266 (pt0) REVERT: G 112 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7819 (m) REVERT: H 112 THR cc_start: 0.7035 (OUTLIER) cc_final: 0.6717 (t) REVERT: H 128 ASP cc_start: 0.5832 (t0) cc_final: 0.5541 (t0) REVERT: H 195 GLU cc_start: 0.5872 (mm-30) cc_final: 0.5283 (tm-30) REVERT: H 268 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6888 (mtmt) REVERT: I 13 HIS cc_start: 0.7008 (m-70) cc_final: 0.6631 (m-70) REVERT: I 140 MET cc_start: 0.6217 (tpt) cc_final: 0.5933 (tpt) REVERT: I 164 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6970 (mp0) REVERT: I 255 GLU cc_start: 0.4762 (mt-10) cc_final: 0.4360 (tm-30) REVERT: I 292 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5540 (tt) REVERT: I 310 ASP cc_start: 0.7014 (t0) cc_final: 0.6623 (t0) REVERT: J 73 SER cc_start: 0.7940 (t) cc_final: 0.7650 (t) REVERT: J 151 LYS cc_start: 0.7016 (tttt) cc_final: 0.6742 (ttpt) REVERT: J 278 VAL cc_start: 0.8178 (m) cc_final: 0.7858 (p) REVERT: a 58 SER cc_start: 0.8161 (p) cc_final: 0.7797 (m) REVERT: a 60 LYS cc_start: 0.6984 (mttp) cc_final: 0.5625 (mmmt) REVERT: a 453 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6790 (mp) REVERT: a 651 TRP cc_start: 0.7267 (OUTLIER) cc_final: 0.6900 (t60) REVERT: c 90 MET cc_start: 0.4473 (tmm) cc_final: 0.3879 (tmt) outliers start: 77 outliers final: 45 residues processed: 363 average time/residue: 0.6435 time to fit residues: 291.2956 Evaluate side-chains 346 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 651 TRP Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 228 ARG Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 261 ASP Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 337 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 312 GLN Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 132 LYS Chi-restraints excluded: chain a residue 397 LYS Chi-restraints excluded: chain a residue 453 ILE Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 604 THR Chi-restraints excluded: chain a residue 651 TRP Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 94 optimal weight: 0.0980 chunk 356 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 305 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 GLN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 ASN I 312 GLN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 ASN J 312 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.202956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.160802 restraints weight = 37905.685| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.78 r_work: 0.4003 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.248 38194 Z= 0.178 Angle : 1.045 78.177 52790 Z= 0.350 Chirality : 0.045 0.189 5258 Planarity : 0.005 0.065 6529 Dihedral : 15.964 179.978 6539 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.19 % Allowed : 21.20 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % 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: -0.27 (0.13), residues: 3928 helix: 0.50 (0.14), residues: 1381 sheet: 0.37 (0.16), residues: 1000 loop : -1.09 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 224 TYR 0.036 0.002 TYR H 345 PHE 0.057 0.002 PHE E 243 TRP 0.053 0.002 TRP I 239 HIS 0.011 0.002 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (38054) covalent geometry : angle 0.85607 / 0.35 (52754) hydrogen bonds : bond 0.04011 / 2.67 ( 1705) hydrogen bonds : angle 5.08940 / 3.59 ( 4806) metal coordination : bond 0.01499 / 1.01 ( 12) metal coordination : angle 22.96787 / 11.63 ( 36) Misc. bond : bond 0.05799 / 3.88 ( 128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20378.78 seconds wall clock time: 345 minutes 29.98 seconds (20729.98 seconds total)