Starting phenix.real_space_refine on Tue Sep 15 07:58:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z6q_14528/09_2026/7z6q_14528_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z6q_14528/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7z6q_14528/09_2026/7z6q_14528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z6q_14528/09_2026/7z6q_14528.map" model { file = "/net/cci-nas-00/data/ceres_data/7z6q_14528/09_2026/7z6q_14528_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z6q_14528/09_2026/7z6q_14528_neut.cif" } 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-2.2.1-6174/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, 1171 Unusual residues: {' CA': 1, 'BCL': 12, 'CLA': 2, 'F39': 1, 'GS0': 1, 'IKV': 1, 'LHG': 2, 'SF4': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} 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, 1163 Unusual residues: {' CA': 1, 'BCL': 12, 'CLA': 2, 'F39': 1, 'GS0': 1, 'IKV': 1, 'LHG': 2} Classifications: {'undetermined': 20} Link IDs: {None: 19} 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: 7.15, per 1000 atoms: 0.20 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: 3.21 Conformation dependent library (CDL) restraints added in 1.2 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: 0.66 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: 6.67 Time building geometry restraints manager: 4.05 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.740 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.600 ------------------------------------------------------------------------------- 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 : 0.964 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: 0.7654 (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: 0.6392 time to fit residues: 566.3004 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 : 1.201 ------------------------------------------------------------------------------- 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: 0.7980 chunk 298 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 = 0.4769 r_free = 0.4769 target = 0.211859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.169810 restraints weight = 38185.225| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 1.77 r_work: 0.4099 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3980 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4013 r_free = 0.4013 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4013 r_free = 0.4013 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.278 38194 Z= 0.191 Angle : 1.077 73.086 52790 Z= 0.381 Chirality : 0.047 0.184 5258 Planarity : 0.005 0.047 6529 Dihedral : 17.564 179.992 6547 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.78 % Rotamer: Outliers : 2.86 % Allowed : 12.32 % Favored : 84.82 % 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: -0.01 (0.14), residues: 1428 sheet: 0.62 (0.16), residues: 1010 loop : -0.79 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 224 TYR 0.020 0.002 TYR A 599 PHE 0.033 0.002 PHE H 243 TRP 0.035 0.002 TRP D 23 HIS 0.010 0.002 HIS H 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (38054) covalent geometry : angle 0.90083 / 0.38 (52754) hydrogen bonds : bond 0.04831 / 3.23 ( 1705) hydrogen bonds : angle 6.10375 / 4.31 ( 4806) metal coordination : bond 0.01257 / 0.87 ( 12) metal coordination : angle 22.63347 / 11.59 ( 36) Misc. bond : bond 0.06447 / 3.84 ( 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 509 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 415 time to evaluate : 1.126 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: 0.6233 (ttp-170) cc_final: 0.5791 (mmp-170) REVERT: A 258 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7017 (mp) REVERT: A 311 LYS cc_start: 0.7642 (tmtt) cc_final: 0.7158 (tttt) REVERT: A 344 LYS cc_start: 0.7825 (pttt) cc_final: 0.7131 (ptmm) REVERT: A 532 TYR cc_start: 0.7070 (m-80) cc_final: 0.6691 (m-80) REVERT: A 570 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7592 (ttp) REVERT: A 640 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6454 (mt-10) REVERT: B 160 LYS cc_start: 0.7277 (ptmm) cc_final: 0.7023 (ptmt) REVERT: B 208 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6860 (t80) REVERT: C 92 MET cc_start: 0.5204 (mtp) cc_final: 0.4950 (mtm) REVERT: C 99 TYR cc_start: 0.6330 (t80) cc_final: 0.5611 (t80) REVERT: D 136 TYR cc_start: 0.6945 (m-80) cc_final: 0.6091 (m-10) REVERT: E 255 GLU cc_start: 0.8343 (tt0) cc_final: 0.7948 (mp0) REVERT: E 268 LYS cc_start: 0.7874 (pttt) cc_final: 0.7366 (ttpp) REVERT: E 322 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.5654 (pttt) REVERT: G 99 VAL cc_start: 0.7851 (t) cc_final: 0.7447 (p) REVERT: G 155 ASP cc_start: 0.7376 (m-30) cc_final: 0.6990 (t0) REVERT: G 193 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8081 (mm) REVERT: H 147 ASP cc_start: 0.5545 (OUTLIER) cc_final: 0.5198 (m-30) REVERT: H 211 GLU cc_start: 0.4070 (OUTLIER) cc_final: 0.3742 (tt0) REVERT: H 285 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.4964 (ttm-80) REVERT: I 292 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.5300 (tt) REVERT: I 329 GLN cc_start: 0.5788 (pm20) cc_final: 0.5375 (mp10) REVERT: I 360 PHE cc_start: 0.6955 (t80) cc_final: 0.6716 (t80) REVERT: J 64 PHE cc_start: 0.6021 (OUTLIER) cc_final: 0.5318 (m-10) REVERT: J 156 ASN cc_start: 0.6798 (m-40) cc_final: 0.6244 (m110) REVERT: J 278 VAL cc_start: 0.8071 (m) cc_final: 0.7721 (p) REVERT: J 312 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.5788 (tm-30) outliers start: 94 outliers final: 41 residues processed: 473 average time/residue: 0.6199 time to fit residues: 362.2952 Evaluate side-chains 388 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 567 ILE Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 584 SER 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 205 VAL Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 232 MET 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: 7.9990 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 317 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 37 ASN ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 ASN I 80 ASN I 157 ASN I 306 ASN J 133 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 74 GLN a 263 ASN a 418 GLN a 587 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.207248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.164578 restraints weight = 38080.755| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 1.77 r_work: 0.4036 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.275 38194 Z= 0.179 Angle : 1.039 76.729 52790 Z= 0.353 Chirality : 0.045 0.189 5258 Planarity : 0.005 0.043 6529 Dihedral : 16.620 179.988 6541 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.35 % Allowed : 14.39 % Favored : 82.26 % 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: -0.12 (0.13), residues: 3928 helix: 0.28 (0.14), residues: 1426 sheet: 0.62 (0.16), residues: 1000 loop : -0.79 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 176 TYR 0.021 0.002 TYR H 345 PHE 0.035 0.002 PHE E 243 TRP 0.031 0.002 TRP I 163 HIS 0.013 0.002 HIS H 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (38054) covalent geometry : angle 0.85371 / 0.35 (52754) hydrogen bonds : bond 0.04342 / 2.89 ( 1705) hydrogen bonds : angle 5.49112 / 3.88 ( 4806) metal coordination : bond 0.01472 / 0.99 ( 12) metal coordination : angle 22.71847 / 11.46 ( 36) Misc. bond : bond 0.06323 / 3.98 ( 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 475 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 365 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.6827 (mp) REVERT: A 344 LYS cc_start: 0.7841 (pttt) cc_final: 0.7227 (pttp) REVERT: A 532 TYR cc_start: 0.7217 (m-80) cc_final: 0.6844 (m-80) REVERT: A 570 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7671 (ttp) REVERT: B 214 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: C 92 MET cc_start: 0.5140 (mtp) cc_final: 0.4914 (mtm) REVERT: C 99 TYR cc_start: 0.6414 (t80) cc_final: 0.5675 (t80) REVERT: D 111 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.6078 (mtpt) REVERT: D 134 LYS cc_start: 0.5144 (ttpt) cc_final: 0.4572 (ptpp) REVERT: D 136 TYR cc_start: 0.6951 (m-80) cc_final: 0.6731 (m-80) REVERT: E 125 TYR cc_start: 0.7916 (p90) cc_final: 0.7642 (p90) REVERT: E 140 MET cc_start: 0.6908 (mtp) cc_final: 0.6215 (mpm) REVERT: E 255 GLU cc_start: 0.8268 (tt0) cc_final: 0.7972 (mp0) REVERT: E 261 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7536 (p0) REVERT: E 268 LYS cc_start: 0.7972 (pttt) cc_final: 0.7409 (ttpt) REVERT: E 322 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5671 (pttt) REVERT: F 140 MET cc_start: 0.7826 (mmm) cc_final: 0.7420 (tpt) REVERT: F 286 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7216 (ttm170) REVERT: G 91 GLU cc_start: 0.7993 (tp30) cc_final: 0.7765 (tt0) REVERT: G 155 ASP cc_start: 0.7464 (m-30) cc_final: 0.7130 (t0) REVERT: G 193 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8231 (mm) REVERT: H 195 GLU cc_start: 0.5823 (mm-30) cc_final: 0.5381 (tm-30) REVERT: H 211 GLU cc_start: 0.4108 (OUTLIER) cc_final: 0.3700 (tt0) REVERT: H 268 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6691 (mtmt) REVERT: I 211 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6092 (pp20) REVERT: I 255 GLU cc_start: 0.5000 (mt-10) cc_final: 0.4605 (tm-30) REVERT: I 292 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5503 (tt) REVERT: I 329 GLN cc_start: 0.5835 (pm20) cc_final: 0.5531 (mp10) REVERT: J 73 SER cc_start: 0.7897 (t) cc_final: 0.7615 (t) REVERT: J 278 VAL cc_start: 0.8145 (m) cc_final: 0.7742 (p) REVERT: J 312 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6007 (tm-30) REVERT: a 60 LYS cc_start: 0.6885 (mttp) cc_final: 0.5208 (tptp) REVERT: a 176 ARG cc_start: 0.5864 (ptm-80) cc_final: 0.5538 (tmm160) REVERT: a 651 TRP cc_start: 0.7245 (OUTLIER) cc_final: 0.6789 (t60) REVERT: c 90 MET cc_start: 0.3907 (tmm) cc_final: 0.3490 (tmt) outliers start: 110 outliers final: 48 residues processed: 435 average time/residue: 0.6396 time to fit residues: 340.9865 Evaluate side-chains 375 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 313 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 258 ILE Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 570 MET 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 209 SER Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 63 ILE 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 160 ILE 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 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 F residue 286 ARG 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 H residue 14 SER 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 232 MET 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 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 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 108 ASP Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 237 SER 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: 0.9990 chunk 274 optimal weight: 0.7980 chunk 387 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 257 optimal weight: 0.0040 chunk 263 optimal weight: 20.0000 chunk 361 optimal weight: 0.9980 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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 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** G 305 ASN G 312 GLN ** H 144 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 156 ASN J 306 ASN J 312 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.209092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.166417 restraints weight = 37938.376| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 1.63 r_work: 0.4093 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3980 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3409 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= 0.133 Angle : 0.974 74.443 52790 Z= 0.318 Chirality : 0.043 0.158 5258 Planarity : 0.004 0.055 6529 Dihedral : 16.003 179.973 6539 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.22 % Allowed : 16.43 % Favored : 80.35 % 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: 0.07 (0.13), residues: 3928 helix: 0.65 (0.14), residues: 1414 sheet: 0.48 (0.15), residues: 1027 loop : -0.74 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 339 TYR 0.027 0.002 TYR H 345 PHE 0.029 0.001 PHE a 692 TRP 0.031 0.001 TRP I 163 HIS 0.011 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (38054) covalent geometry : angle 0.77956 / 0.31 (52754) hydrogen bonds : bond 0.03687 / 2.47 ( 1705) hydrogen bonds : angle 5.17273 / 3.68 ( 4806) metal coordination : bond 0.00951 / 0.61 ( 12) metal coordination : angle 22.35722 / 11.31 ( 36) Misc. bond : bond 0.05874 / 3.79 ( 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 454 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 348 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6318 (ttp-170) cc_final: 0.5939 (mmp-170) REVERT: A 344 LYS cc_start: 0.7869 (pttt) cc_final: 0.7287 (pttp) REVERT: A 532 TYR cc_start: 0.7172 (m-80) cc_final: 0.6754 (m-80) REVERT: A 590 HIS cc_start: 0.7487 (m-70) cc_final: 0.6831 (m170) REVERT: B 214 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: B 227 HIS cc_start: 0.6112 (OUTLIER) cc_final: 0.5511 (t-170) REVERT: C 92 MET cc_start: 0.5247 (mtp) cc_final: 0.5000 (mtm) REVERT: D 111 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.5804 (ttpt) REVERT: D 134 LYS cc_start: 0.5165 (ttpt) cc_final: 0.4606 (ptpp) REVERT: E 140 MET cc_start: 0.6776 (mtp) cc_final: 0.6123 (mpm) REVERT: E 322 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.5762 (pttt) REVERT: F 140 MET cc_start: 0.7883 (mmm) cc_final: 0.7504 (tpt) REVERT: F 286 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7430 (ttm170) REVERT: G 155 ASP cc_start: 0.7449 (m-30) cc_final: 0.7137 (t0) REVERT: H 195 GLU cc_start: 0.5765 (mm-30) cc_final: 0.5361 (tm-30) REVERT: H 211 GLU cc_start: 0.4313 (OUTLIER) cc_final: 0.3828 (tt0) REVERT: H 268 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6674 (mtmt) REVERT: H 335 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5629 (tt) REVERT: I 150 MET cc_start: 0.7152 (mtp) cc_final: 0.6691 (mtm) REVERT: I 255 GLU cc_start: 0.5007 (mt-10) cc_final: 0.4570 (tm-30) REVERT: I 270 ASP cc_start: 0.5059 (p0) cc_final: 0.4616 (p0) REVERT: I 292 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5456 (tt) REVERT: I 329 GLN cc_start: 0.5850 (pm20) cc_final: 0.5542 (mp10) REVERT: J 73 SER cc_start: 0.7863 (t) cc_final: 0.7536 (t) REVERT: J 103 MET cc_start: 0.6027 (tmm) cc_final: 0.5788 (ptp) REVERT: J 278 VAL cc_start: 0.8116 (m) cc_final: 0.7740 (p) REVERT: J 312 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6025 (tm130) REVERT: a 60 LYS cc_start: 0.6896 (mttp) cc_final: 0.5624 (mmmt) REVERT: a 275 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7217 (ttm) REVERT: a 450 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: a 651 TRP cc_start: 0.7265 (OUTLIER) cc_final: 0.6747 (t60) REVERT: c 90 MET cc_start: 0.4179 (tmm) cc_final: 0.3645 (tmt) outliers start: 106 outliers final: 43 residues processed: 415 average time/residue: 0.6037 time to fit residues: 310.4295 Evaluate side-chains 361 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 305 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 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 170 PHE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 55 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 160 ILE 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 F residue 222 ARG Chi-restraints excluded: chain F residue 286 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 265 ILE Chi-restraints excluded: chain H residue 14 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 103 MET 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 J residue 99 VAL Chi-restraints excluded: chain J residue 108 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 274 ASP Chi-restraints excluded: chain a residue 275 MET Chi-restraints excluded: chain a residue 450 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 4 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 303 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 338 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 180 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 133 ASN D 140 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** ** H 306 ASN ** 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 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.201353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.158711 restraints weight = 38253.647| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 1.80 r_work: 0.3974 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.312 38194 Z= 0.269 Angle : 1.150 79.911 52790 Z= 0.398 Chirality : 0.050 0.249 5258 Planarity : 0.006 0.060 6529 Dihedral : 16.462 179.997 6539 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.80 % Allowed : 16.55 % Favored : 79.65 % 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: -0.47 (0.13), residues: 3928 helix: 0.08 (0.13), residues: 1398 sheet: 0.30 (0.15), residues: 1041 loop : -1.00 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 96 TYR 0.031 0.003 TYR a 202 PHE 0.039 0.003 PHE E 243 TRP 0.025 0.002 TRP A 513 HIS 0.015 0.003 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.27 (38054) covalent geometry : angle 0.96639 / 0.39 (52754) hydrogen bonds : bond 0.04719 / 3.12 ( 1705) hydrogen bonds : angle 5.40784 / 3.82 ( 4806) metal coordination : bond 0.02517 / 1.76 ( 12) metal coordination : angle 23.86889 / 12.37 ( 36) Misc. bond : bond 0.06984 / 4.57 ( 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 441 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 316 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.7908 (pttt) cc_final: 0.7307 (pttp) REVERT: A 590 HIS cc_start: 0.7751 (m-70) cc_final: 0.7208 (m170) REVERT: B 135 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7466 (mm) REVERT: B 227 HIS cc_start: 0.6201 (OUTLIER) cc_final: 0.5630 (t-170) REVERT: C 76 LYS cc_start: 0.6114 (tmtt) cc_final: 0.5534 (ttmt) REVERT: C 99 TYR cc_start: 0.6339 (t80) cc_final: 0.5613 (t80) REVERT: D 111 LYS cc_start: 0.6343 (OUTLIER) cc_final: 0.6086 (mtpt) REVERT: D 134 LYS cc_start: 0.5288 (ttpt) cc_final: 0.4700 (ptpp) REVERT: D 136 TYR cc_start: 0.7000 (m-80) cc_final: 0.6774 (m-80) REVERT: E 322 LYS cc_start: 0.6352 (OUTLIER) cc_final: 0.5782 (pttt) REVERT: F 222 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7465 (ttp-170) REVERT: F 286 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7041 (ttm170) REVERT: G 112 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7702 (m) REVERT: H 195 GLU cc_start: 0.5868 (mm-30) cc_final: 0.5451 (tm-30) REVERT: H 211 GLU cc_start: 0.4413 (OUTLIER) cc_final: 0.3744 (tt0) REVERT: H 246 ASP cc_start: 0.6531 (p0) cc_final: 0.6077 (m-30) REVERT: H 268 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6768 (mtmt) REVERT: H 335 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5586 (tt) REVERT: I 255 GLU cc_start: 0.4943 (mt-10) cc_final: 0.4586 (tm-30) REVERT: I 270 ASP cc_start: 0.5357 (p0) cc_final: 0.4902 (p0) REVERT: I 292 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5625 (tt) REVERT: I 331 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.4957 (mtm-85) REVERT: J 73 SER cc_start: 0.7919 (t) cc_final: 0.7615 (t) REVERT: J 278 VAL cc_start: 0.8174 (m) cc_final: 0.7838 (p) REVERT: a 60 LYS cc_start: 0.7055 (mttp) cc_final: 0.5749 (mmmt) REVERT: a 453 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6743 (mp) REVERT: a 651 TRP cc_start: 0.7300 (OUTLIER) cc_final: 0.6905 (t60) REVERT: c 90 MET cc_start: 0.4176 (tmm) cc_final: 0.3689 (tmt) outliers start: 125 outliers final: 59 residues processed: 401 average time/residue: 0.5931 time to fit residues: 295.5218 Evaluate side-chains 362 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 289 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 131 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 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 170 PHE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 227 HIS 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 82 THR Chi-restraints excluded: chain D residue 111 LYS Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 322 LYS 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 286 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 278 VAL Chi-restraints excluded: chain H residue 14 SER 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 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 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 331 ARG Chi-restraints excluded: chain J residue 17 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 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 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 356 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 364 optimal weight: 5.9990 chunk 365 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 317 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 ASN ** 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 = 0.4697 r_free = 0.4697 target = 0.204449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.161292 restraints weight = 38062.378| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 1.77 r_work: 0.4006 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 4.09 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 = 0.84 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 = 0.85 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: 0.7607 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 38194 Z= 0.154 Angle : 1.014 76.916 52790 Z= 0.333 Chirality : 0.044 0.162 5258 Planarity : 0.004 0.051 6529 Dihedral : 16.022 179.990 6539 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.26 % Allowed : 17.95 % Favored : 78.80 % 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: -0.17 (0.13), residues: 3928 helix: 0.46 (0.14), residues: 1410 sheet: 0.37 (0.16), residues: 1035 loop : -0.92 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 224 TYR 0.027 0.002 TYR H 345 PHE 0.027 0.002 PHE a 692 TRP 0.018 0.001 TRP c 52 HIS 0.010 0.002 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (38054) covalent geometry : angle 0.81882 / 0.33 (52754) hydrogen bonds : bond 0.03896 / 2.60 ( 1705) hydrogen bonds : angle 5.11384 / 3.62 ( 4806) metal coordination : bond 0.01194 / 0.80 ( 12) metal coordination : angle 22.93093 / 11.69 ( 36) Misc. bond : bond 0.05854 / 3.85 ( 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 421 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 314 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7837 (ptpt) cc_final: 0.7491 (tttm) REVERT: A 110 ASP cc_start: 0.6491 (t0) cc_final: 0.6268 (t0) REVERT: A 114 TYR cc_start: 0.6205 (t80) cc_final: 0.5532 (t80) REVERT: A 177 CYS cc_start: 0.7438 (t) cc_final: 0.7188 (t) REVERT: A 344 LYS cc_start: 0.7861 (pttt) cc_final: 0.7242 (pttp) REVERT: A 471 PHE cc_start: 0.7989 (m-80) cc_final: 0.7676 (m-80) REVERT: A 590 HIS cc_start: 0.7742 (m-70) cc_final: 0.7149 (m170) REVERT: B 137 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: C 76 LYS cc_start: 0.6100 (tmtt) cc_final: 0.5564 (ttmt) REVERT: D 134 LYS cc_start: 0.5370 (ttpt) cc_final: 0.4839 (ptpp) REVERT: E 140 MET cc_start: 0.6763 (mtp) cc_final: 0.6074 (mpm) REVERT: F 140 MET cc_start: 0.7996 (mmm) cc_final: 0.7545 (tpt) REVERT: F 222 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7360 (ttp-170) REVERT: F 286 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7241 (ttm170) REVERT: G 112 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7657 (m) REVERT: H 195 GLU cc_start: 0.5819 (mm-30) cc_final: 0.5427 (tm-30) REVERT: H 211 GLU cc_start: 0.4347 (OUTLIER) cc_final: 0.3663 (tt0) REVERT: H 246 ASP cc_start: 0.6557 (p0) cc_final: 0.6073 (m-30) REVERT: H 268 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6747 (mtmt) REVERT: H 335 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5644 (tt) REVERT: I 147 ASP cc_start: 0.6722 (m-30) cc_final: 0.6174 (t70) REVERT: I 150 MET cc_start: 0.6905 (mtp) cc_final: 0.6487 (mtm) REVERT: I 255 GLU cc_start: 0.4793 (mt-10) cc_final: 0.4474 (tm-30) REVERT: I 270 ASP cc_start: 0.5285 (p0) cc_final: 0.4811 (OUTLIER) REVERT: I 292 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5600 (tt) REVERT: J 73 SER cc_start: 0.7905 (t) cc_final: 0.7596 (t) REVERT: J 278 VAL cc_start: 0.8164 (m) cc_final: 0.7831 (p) REVERT: a 60 LYS cc_start: 0.7004 (mttp) cc_final: 0.5303 (tptp) REVERT: a 453 ILE cc_start: 0.7138 (OUTLIER) cc_final: 0.6716 (mp) REVERT: a 651 TRP cc_start: 0.7260 (OUTLIER) cc_final: 0.6870 (t60) REVERT: c 90 MET cc_start: 0.4135 (tmm) cc_final: 0.3662 (tmt) REVERT: c 94 LEU cc_start: 0.3449 (tp) cc_final: 0.2994 (tt) outliers start: 107 outliers final: 61 residues processed: 391 average time/residue: 0.6068 time to fit residues: 295.9343 Evaluate side-chains 359 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 289 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 651 TRP Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 209 SER 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 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 64 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 286 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 H residue 14 SER Chi-restraints excluded: chain H residue 106 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 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 209 ASN 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 293 ILE Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 331 ARG 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 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 635 ARG Chi-restraints excluded: chain a residue 651 TRP 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: 0.0270 chunk 171 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 164 optimal weight: 0.0470 chunk 181 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 140 GLN ** E 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 GLN F 157 ASN ** 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 312 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.207570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.165056 restraints weight = 38113.029| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 1.76 r_work: 0.4054 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3936 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.260 38194 Z= 0.123 Angle : 0.960 74.569 52790 Z= 0.309 Chirality : 0.042 0.173 5258 Planarity : 0.004 0.053 6529 Dihedral : 15.537 179.998 6539 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.56 % Allowed : 19.26 % Favored : 78.19 % 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: 0.79 (0.14), residues: 1430 sheet: 0.43 (0.16), residues: 1035 loop : -0.84 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 224 TYR 0.029 0.001 TYR H 345 PHE 0.029 0.001 PHE a 180 TRP 0.019 0.001 TRP c 52 HIS 0.009 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (38054) covalent geometry : angle 0.76247 / 0.30 (52754) hydrogen bonds : bond 0.03489 / 2.34 ( 1705) hydrogen bonds : angle 4.87882 / 3.46 ( 4806) metal coordination : bond 0.00775 / 0.49 ( 12) metal coordination : angle 22.37405 / 11.35 ( 36) Misc. bond : bond 0.05664 / 3.68 ( 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 406 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 322 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.6135 (mp) REVERT: A 344 LYS cc_start: 0.7808 (pttt) cc_final: 0.7183 (pttp) REVERT: A 471 PHE cc_start: 0.8034 (m-80) cc_final: 0.7764 (m-80) REVERT: A 590 HIS cc_start: 0.7673 (m-70) cc_final: 0.7106 (m170) REVERT: B 135 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7227 (mm) REVERT: B 137 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: C 76 LYS cc_start: 0.6004 (tmtt) cc_final: 0.5460 (ttmt) REVERT: C 92 MET cc_start: 0.5560 (mtm) cc_final: 0.3580 (ptm) REVERT: D 114 MET cc_start: 0.7849 (ttp) cc_final: 0.7400 (ttt) REVERT: D 134 LYS cc_start: 0.5395 (ttpt) cc_final: 0.4861 (ptpp) REVERT: E 140 MET cc_start: 0.6674 (mtp) cc_final: 0.6018 (mpm) REVERT: E 191 THR cc_start: 0.8067 (m) cc_final: 0.7616 (p) REVERT: F 140 MET cc_start: 0.8018 (mmm) cc_final: 0.7560 (tpt) REVERT: F 253 GLN cc_start: 0.7433 (pt0) cc_final: 0.7181 (pt0) REVERT: F 286 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7375 (ttm170) REVERT: G 112 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7717 (m) REVERT: H 128 ASP cc_start: 0.5971 (t0) cc_final: 0.5635 (t0) REVERT: H 195 GLU cc_start: 0.5804 (mm-30) cc_final: 0.5478 (tm-30) REVERT: H 246 ASP cc_start: 0.6577 (p0) cc_final: 0.6068 (m-30) REVERT: H 268 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6772 (mtmt) REVERT: H 300 MET cc_start: 0.7549 (mtp) cc_final: 0.7248 (mtp) REVERT: H 335 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5749 (tt) REVERT: I 13 HIS cc_start: 0.6756 (m-70) cc_final: 0.6413 (m-70) REVERT: I 150 MET cc_start: 0.6807 (mtp) cc_final: 0.6398 (mtm) REVERT: I 255 GLU cc_start: 0.4712 (mt-10) cc_final: 0.4385 (tm-30) REVERT: I 270 ASP cc_start: 0.5310 (p0) cc_final: 0.4788 (p0) REVERT: I 292 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5478 (tt) REVERT: J 73 SER cc_start: 0.7918 (t) cc_final: 0.7618 (t) REVERT: J 116 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7502 (tm-30) REVERT: J 147 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.5849 (m-30) REVERT: J 278 VAL cc_start: 0.8144 (m) cc_final: 0.7768 (p) REVERT: J 321 TYR cc_start: 0.6531 (m-10) cc_final: 0.6289 (m-10) REVERT: a 176 ARG cc_start: 0.5815 (ptm-80) cc_final: 0.5381 (tmm160) REVERT: a 453 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6592 (mp) REVERT: a 651 TRP cc_start: 0.7259 (OUTLIER) cc_final: 0.6857 (t60) REVERT: c 90 MET cc_start: 0.4205 (tmm) cc_final: 0.3690 (tmt) outliers start: 84 outliers final: 45 residues processed: 385 average time/residue: 0.5725 time to fit residues: 277.7988 Evaluate side-chains 347 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 291 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 567 ILE Chi-restraints excluded: chain A residue 570 MET 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 701 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 GLU 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 E residue 8 ASP 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 161 ASP Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 286 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 245 SER Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 268 LYS 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 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 331 ARG Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 132 LYS 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 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 341 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 chunk 328 optimal weight: 0.4980 chunk 267 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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** E 312 GLN 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 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 GLN a 418 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.203779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.161289 restraints weight = 37990.915| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 1.76 r_work: 0.4002 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 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: 0.3891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.255 38194 Z= 0.187 Angle : 1.036 78.383 52790 Z= 0.345 Chirality : 0.045 0.187 5258 Planarity : 0.005 0.052 6529 Dihedral : 15.799 179.989 6539 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.83 % Allowed : 19.90 % Favored : 77.27 % 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: -0.08 (0.13), residues: 3928 helix: 0.65 (0.14), residues: 1392 sheet: 0.38 (0.16), residues: 1033 loop : -0.96 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 224 TYR 0.032 0.002 TYR H 345 PHE 0.031 0.002 PHE C 53 TRP 0.018 0.002 TRP c 52 HIS 0.013 0.002 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.18 (38054) covalent geometry : angle 0.84495 / 0.34 (52754) hydrogen bonds : bond 0.04007 / 2.66 ( 1705) hydrogen bonds : angle 5.00893 / 3.54 ( 4806) metal coordination : bond 0.01729 / 1.17 ( 12) metal coordination : angle 22.98964 / 11.67 ( 36) Misc. bond : bond 0.05894 / 3.82 ( 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 391 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 298 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6411 (ttp-170) cc_final: 0.5826 (mmm160) REVERT: A 222 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.6226 (mp) REVERT: A 344 LYS cc_start: 0.7874 (pttt) cc_final: 0.7246 (pttp) REVERT: A 590 HIS cc_start: 0.7696 (m-70) cc_final: 0.7167 (m170) REVERT: A 597 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: B 135 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7347 (mm) REVERT: B 137 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: B 214 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: C 76 LYS cc_start: 0.6090 (tmtt) cc_final: 0.5531 (ttmt) REVERT: C 92 MET cc_start: 0.5746 (mtm) cc_final: 0.3647 (ptm) REVERT: D 68 ARG cc_start: 0.6728 (ttp-110) cc_final: 0.6473 (ttp80) REVERT: D 134 LYS cc_start: 0.5418 (ttpt) cc_final: 0.4878 (ptpp) REVERT: E 238 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6591 (ptm160) REVERT: F 140 MET cc_start: 0.8002 (mmm) cc_final: 0.7562 (tpt) REVERT: F 222 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7350 (ttp-170) REVERT: F 253 GLN cc_start: 0.7503 (pt0) cc_final: 0.7246 (pt0) REVERT: F 286 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7322 (ttm170) REVERT: G 112 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (m) REVERT: H 128 ASP cc_start: 0.5976 (t0) cc_final: 0.5652 (t0) REVERT: H 195 GLU cc_start: 0.5917 (mm-30) cc_final: 0.5550 (tm-30) REVERT: H 246 ASP cc_start: 0.6569 (p0) cc_final: 0.6118 (m-30) REVERT: H 268 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6848 (mtmt) REVERT: H 314 LYS cc_start: 0.7636 (tttt) cc_final: 0.6729 (tppp) REVERT: H 335 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5724 (tt) REVERT: I 13 HIS cc_start: 0.6847 (m-70) cc_final: 0.6505 (m-70) REVERT: I 255 GLU cc_start: 0.4819 (mt-10) cc_final: 0.4408 (tm-30) REVERT: I 292 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5579 (tt) REVERT: J 73 SER cc_start: 0.7999 (t) cc_final: 0.7683 (t) REVERT: J 116 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7569 (tm-30) REVERT: J 278 VAL cc_start: 0.8173 (m) cc_final: 0.7823 (p) REVERT: J 339 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.6509 (mtt90) REVERT: a 60 LYS cc_start: 0.6944 (mttp) cc_final: 0.5679 (mmmt) REVERT: a 453 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6692 (mp) REVERT: a 651 TRP cc_start: 0.7302 (OUTLIER) cc_final: 0.6922 (t60) REVERT: a 654 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6513 (mtpt) REVERT: c 90 MET cc_start: 0.4292 (tmm) cc_final: 0.3751 (tmt) outliers start: 93 outliers final: 54 residues processed: 362 average time/residue: 0.5822 time to fit residues: 262.8731 Evaluate side-chains 356 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 287 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 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 135 ILE Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 214 GLU 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 D residue 98 GLU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 238 ARG 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 286 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 14 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 268 LYS 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 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 331 ARG Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 321 TYR Chi-restraints excluded: chain a residue 58 SER Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR 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 453 ILE Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 635 ARG Chi-restraints excluded: chain a residue 651 TRP Chi-restraints excluded: chain a residue 654 LYS 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: 2.9990 chunk 167 optimal weight: 6.9990 chunk 371 optimal weight: 0.9990 chunk 238 optimal weight: 0.7980 chunk 330 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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** ** 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 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 305 ASN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 GLN a 418 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.206692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.164010 restraints weight = 38032.934| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 1.75 r_work: 0.4035 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.267 38194 Z= 0.129 Angle : 0.969 75.635 52790 Z= 0.314 Chirality : 0.043 0.176 5258 Planarity : 0.004 0.053 6529 Dihedral : 15.502 179.986 6539 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.34 % Allowed : 20.75 % Favored : 76.91 % 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: 0.84 (0.14), residues: 1418 sheet: 0.39 (0.15), residues: 1037 loop : -0.84 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 224 TYR 0.034 0.002 TYR H 345 PHE 0.039 0.001 PHE E 243 TRP 0.018 0.001 TRP c 52 HIS 0.012 0.001 HIS H 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (38054) covalent geometry : angle 0.77482 / 0.31 (52754) hydrogen bonds : bond 0.03551 / 2.37 ( 1705) hydrogen bonds : angle 4.82680 / 3.41 ( 4806) metal coordination : bond 0.00852 / 0.53 ( 12) metal coordination : angle 22.32666 / 11.19 ( 36) Misc. bond : bond 0.05464 / 3.66 ( 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 376 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 299 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6345 (ttp-170) cc_final: 0.5899 (mmp-170) REVERT: A 222 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6250 (mp) REVERT: A 344 LYS cc_start: 0.7874 (pttt) cc_final: 0.7212 (pttp) REVERT: A 590 HIS cc_start: 0.7695 (m-70) cc_final: 0.7157 (m170) REVERT: B 135 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7327 (mm) REVERT: B 137 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: C 76 LYS cc_start: 0.5974 (tmtt) cc_final: 0.5432 (ttmt) REVERT: C 92 MET cc_start: 0.5589 (mtm) cc_final: 0.3640 (ptm) REVERT: D 68 ARG cc_start: 0.6732 (ttp-110) cc_final: 0.6485 (tmm160) REVERT: D 134 LYS cc_start: 0.5438 (ttpt) cc_final: 0.4892 (ptpp) REVERT: E 125 TYR cc_start: 0.7922 (p90) cc_final: 0.7571 (p90) REVERT: E 140 MET cc_start: 0.6687 (mtp) cc_final: 0.6029 (mpm) REVERT: E 191 THR cc_start: 0.8058 (m) cc_final: 0.7626 (p) REVERT: E 322 LYS cc_start: 0.6173 (OUTLIER) cc_final: 0.5375 (pttt) REVERT: F 140 MET cc_start: 0.8015 (mmm) cc_final: 0.7559 (tpt) REVERT: F 222 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7369 (ttp-170) REVERT: F 253 GLN cc_start: 0.7482 (pt0) cc_final: 0.7209 (pt0) REVERT: F 286 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7329 (ttm170) REVERT: G 112 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7740 (m) REVERT: H 128 ASP cc_start: 0.5890 (t0) cc_final: 0.5553 (t0) REVERT: H 195 GLU cc_start: 0.5859 (mm-30) cc_final: 0.5477 (tm-30) REVERT: H 246 ASP cc_start: 0.6589 (p0) cc_final: 0.6136 (m-30) REVERT: H 268 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6620 (mptt) REVERT: H 314 LYS cc_start: 0.7620 (tttt) cc_final: 0.6702 (tppp) REVERT: H 335 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5740 (tt) REVERT: H 361 GLU cc_start: 0.6298 (tm-30) cc_final: 0.6033 (tp30) REVERT: I 13 HIS cc_start: 0.6877 (m-70) cc_final: 0.6543 (m-70) REVERT: I 150 MET cc_start: 0.6712 (mtp) cc_final: 0.6351 (mtm) REVERT: I 255 GLU cc_start: 0.4748 (mt-10) cc_final: 0.4413 (tm-30) REVERT: J 73 SER cc_start: 0.7978 (t) cc_final: 0.7680 (t) REVERT: J 116 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7475 (tm-30) REVERT: J 151 LYS cc_start: 0.6898 (tttt) cc_final: 0.6676 (ttpt) REVERT: J 278 VAL cc_start: 0.8128 (m) cc_final: 0.7756 (p) REVERT: J 310 ASP cc_start: 0.6580 (t0) cc_final: 0.6344 (t0) REVERT: a 60 LYS cc_start: 0.6881 (mttp) cc_final: 0.5289 (tptp) REVERT: a 453 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6641 (mp) REVERT: a 651 TRP cc_start: 0.7300 (OUTLIER) cc_final: 0.6880 (t60) REVERT: c 90 MET cc_start: 0.4217 (tmm) cc_final: 0.3709 (tmt) outliers start: 77 outliers final: 46 residues processed: 356 average time/residue: 0.5924 time to fit residues: 262.2824 Evaluate side-chains 346 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 222 ILE 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 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 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 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 98 GLU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 112 THR 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 64 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 286 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 14 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 268 LYS 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 261 ASP Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 331 ARG 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 a residue 100 VAL Chi-restraints excluded: chain a residue 116 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 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 59 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 323 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 337 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.205710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.162801 restraints weight = 38011.787| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 1.76 r_work: 0.4023 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 38194 Z= 0.146 Angle : 0.984 76.320 52790 Z= 0.322 Chirality : 0.043 0.174 5258 Planarity : 0.004 0.053 6529 Dihedral : 15.480 179.986 6539 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.22 % Allowed : 21.08 % Favored : 76.70 % 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: 0.08 (0.13), residues: 3928 helix: 0.82 (0.14), residues: 1416 sheet: 0.38 (0.15), residues: 1042 loop : -0.85 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 339 TYR 0.035 0.002 TYR H 345 PHE 0.033 0.002 PHE E 243 TRP 0.076 0.002 TRP I 239 HIS 0.012 0.002 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (38054) covalent geometry : angle 0.79080 / 0.32 (52754) hydrogen bonds : bond 0.03652 / 2.43 ( 1705) hydrogen bonds : angle 4.82789 / 3.41 ( 4806) metal coordination : bond 0.01101 / 0.71 ( 12) metal coordination : angle 22.46637 / 11.27 ( 36) Misc. bond : bond 0.05453 / 3.62 ( 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 364 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 1.250 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: A 57 ARG cc_start: 0.6315 (ttp-170) cc_final: 0.5859 (mmp-170) REVERT: A 222 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6212 (mp) REVERT: A 344 LYS cc_start: 0.7889 (pttt) cc_final: 0.7196 (pttp) REVERT: A 590 HIS cc_start: 0.7698 (m-70) cc_final: 0.7181 (m170) REVERT: B 135 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7386 (mm) REVERT: B 137 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: C 76 LYS cc_start: 0.5964 (tmtt) cc_final: 0.5416 (ttmt) REVERT: C 92 MET cc_start: 0.5606 (mtm) cc_final: 0.3637 (ptm) REVERT: D 68 ARG cc_start: 0.6735 (ttp-110) cc_final: 0.6489 (tmm160) REVERT: D 134 LYS cc_start: 0.5403 (ttpt) cc_final: 0.4844 (ptpp) REVERT: E 191 THR cc_start: 0.8081 (m) cc_final: 0.7652 (p) REVERT: E 322 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5373 (pttt) REVERT: F 140 MET cc_start: 0.8005 (mmm) cc_final: 0.7565 (tpt) REVERT: F 222 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7379 (ttp-170) REVERT: F 253 GLN cc_start: 0.7505 (pt0) cc_final: 0.7228 (pt0) REVERT: F 286 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7321 (ttm170) REVERT: G 112 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7774 (m) REVERT: H 128 ASP cc_start: 0.5898 (t0) cc_final: 0.5584 (t0) REVERT: H 268 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6597 (mptt) REVERT: H 314 LYS cc_start: 0.7622 (tttt) cc_final: 0.6707 (tppp) REVERT: H 335 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5736 (tt) REVERT: H 361 GLU cc_start: 0.6285 (tm-30) cc_final: 0.6018 (tp30) REVERT: I 13 HIS cc_start: 0.6913 (m-70) cc_final: 0.6493 (m-70) REVERT: I 150 MET cc_start: 0.6716 (mtp) cc_final: 0.6501 (mtm) REVERT: I 255 GLU cc_start: 0.4758 (mt-10) cc_final: 0.4344 (tm-30) REVERT: I 310 ASP cc_start: 0.6938 (t0) cc_final: 0.6559 (t0) REVERT: J 73 SER cc_start: 0.7983 (t) cc_final: 0.7680 (t) REVERT: J 116 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7523 (tm-30) REVERT: J 151 LYS cc_start: 0.6900 (tttt) cc_final: 0.6689 (ttpt) REVERT: J 278 VAL cc_start: 0.8115 (m) cc_final: 0.7736 (p) REVERT: a 60 LYS cc_start: 0.6942 (mttp) cc_final: 0.5336 (tptp) REVERT: a 453 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6671 (mp) REVERT: a 651 TRP cc_start: 0.7303 (OUTLIER) cc_final: 0.6876 (t60) REVERT: c 90 MET cc_start: 0.4371 (tmm) cc_final: 0.3834 (tmt) outliers start: 73 outliers final: 48 residues processed: 345 average time/residue: 0.5936 time to fit residues: 255.9358 Evaluate side-chains 347 residues out of total 3287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 222 ILE 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 618 MET 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 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 112 THR 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 64 PHE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 286 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 14 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 268 LYS 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 261 ASP Chi-restraints excluded: chain I residue 293 ILE Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 331 ARG 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 a residue 100 VAL Chi-restraints excluded: chain a residue 116 THR 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 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 94 optimal weight: 0.7980 chunk 356 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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** ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.203681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.159513 restraints weight = 37849.796| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.68 r_work: 0.4014 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3933 r_free = 0.3933 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3933 r_free = 0.3933 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.262 38194 Z= 0.178 Angle : 1.031 78.424 52790 Z= 0.343 Chirality : 0.045 0.183 5258 Planarity : 0.005 0.054 6529 Dihedral : 15.651 179.976 6539 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.25 % Allowed : 21.11 % Favored : 76.64 % 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: -0.06 (0.13), residues: 3928 helix: 0.73 (0.14), residues: 1392 sheet: 0.34 (0.15), residues: 1046 loop : -0.98 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 339 TYR 0.036 0.002 TYR H 345 PHE 0.036 0.002 PHE E 243 TRP 0.074 0.002 TRP I 239 HIS 0.012 0.002 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.17 (38054) covalent geometry : angle 0.83921 / 0.34 (52754) hydrogen bonds : bond 0.03950 / 2.63 ( 1705) hydrogen bonds : angle 4.92867 / 3.48 ( 4806) metal coordination : bond 0.01542 / 1.03 ( 12) metal coordination : angle 22.94646 / 11.56 ( 36) Misc. bond : bond 0.05853 / 3.91 ( 128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19447.37 seconds wall clock time: 329 minutes 35.10 seconds (19775.10 seconds total)