Starting phenix.real_space_refine (version: dev) on Mon Dec 12 07:24:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0h_8948/12_2022/6e0h_8948_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0h_8948/12_2022/6e0h_8948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0h_8948/12_2022/6e0h_8948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0h_8948/12_2022/6e0h_8948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0h_8948/12_2022/6e0h_8948_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0h_8948/12_2022/6e0h_8948_neut.pdb" } resolution = 4.05 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 647": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "A PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 708": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9524 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4760 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 27, 'TRANS': 558} Chain breaks: 8 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4760 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 27, 'TRANS': 558} Chain breaks: 8 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.78, per 1000 atoms: 0.61 Number of scatterers: 9524 At special positions: 0 Unit cell: (126.051, 75.6309, 99.7451, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 38 16.00 O 1642 8.00 N 1572 7.00 C 6268 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 1.5 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 2 sheets defined 70.0% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 27 through 46 removed outlier: 3.763A pdb=" N GLU B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 86 removed outlier: 3.838A pdb=" N ARG B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 117 removed outlier: 3.844A pdb=" N ILE B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 117 " --> pdb=" O HIS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.664A pdb=" N MET B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP B 155 " --> pdb=" O CYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.705A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.556A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.547A pdb=" N VAL B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.878A pdb=" N MET B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 311 removed outlier: 3.985A pdb=" N ALA B 287 " --> pdb=" O GLN B 283 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 305 " --> pdb=" O CYS B 301 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 348 removed outlier: 3.906A pdb=" N PHE B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Proline residue: B 324 - end of helix removed outlier: 3.741A pdb=" N ILE B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.809A pdb=" N THR B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 384 removed outlier: 4.055A pdb=" N LYS B 359 " --> pdb=" O GLN B 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 374 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Proline residue: B 377 - end of helix removed outlier: 4.053A pdb=" N THR B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.606A pdb=" N ILE B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 removed outlier: 3.569A pdb=" N ILE B 439 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix removed outlier: 3.641A pdb=" N PHE B 456 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.605A pdb=" N ARG B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 525 removed outlier: 3.691A pdb=" N ASP B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 520 " --> pdb=" O CYS B 516 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 553 removed outlier: 3.585A pdb=" N SER B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 591 removed outlier: 3.580A pdb=" N GLY B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 575 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 635 removed outlier: 3.844A pdb=" N SER B 617 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 659 removed outlier: 3.729A pdb=" N ARG B 653 " --> pdb=" O MET B 649 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR B 654 " --> pdb=" O MET B 650 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 658 " --> pdb=" O TYR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 Processing helix chain 'B' and resid 721 through 724 removed outlier: 3.991A pdb=" N THR B 724 " --> pdb=" O SER B 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 721 through 724' Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.762A pdb=" N GLU A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 86 removed outlier: 3.839A pdb=" N ARG A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.845A pdb=" N ILE A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.664A pdb=" N MET A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.705A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.556A pdb=" N PHE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.546A pdb=" N VAL A 214 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.877A pdb=" N MET A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.985A pdb=" N ALA A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 305 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 348 removed outlier: 3.905A pdb=" N PHE A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.740A pdb=" N ILE A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.809A pdb=" N THR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 384 removed outlier: 4.056A pdb=" N LYS A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 374 " --> pdb=" O ASN A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 4.053A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 removed outlier: 3.606A pdb=" N ILE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 removed outlier: 3.569A pdb=" N ILE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix removed outlier: 3.641A pdb=" N PHE A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.605A pdb=" N ARG A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 removed outlier: 3.691A pdb=" N ASP A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 520 " --> pdb=" O CYS A 516 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.585A pdb=" N SER A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 removed outlier: 3.579A pdb=" N GLY A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 575 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 635 removed outlier: 3.844A pdb=" N SER A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 630 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 659 removed outlier: 3.730A pdb=" N ARG A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 654 " --> pdb=" O MET A 650 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 721 through 724 removed outlier: 3.991A pdb=" N THR A 724 " --> pdb=" O SER A 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 721 through 724' Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 21 removed outlier: 8.099A pdb=" N TYR B 18 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ARG B 65 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 20 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE B 63 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL B 62 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 52 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL B 64 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR B 50 " --> pdb=" O VAL B 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 8.099A pdb=" N TYR A 18 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG A 65 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A 20 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 63 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL A 62 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 52 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL A 64 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR A 50 " --> pdb=" O VAL A 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 472 hydrogen bonds defined for protein. 1416 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: 2.57 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2896 1.34 - 1.46: 2123 1.46 - 1.57: 4695 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 9770 Sorted by residual: bond pdb=" CB TYR A 352 " pdb=" CG TYR A 352 " ideal model delta sigma weight residual 1.512 1.455 0.057 2.20e-02 2.07e+03 6.62e+00 bond pdb=" CB TYR B 352 " pdb=" CG TYR B 352 " ideal model delta sigma weight residual 1.512 1.455 0.057 2.20e-02 2.07e+03 6.62e+00 bond pdb=" N ALA B 609 " pdb=" CA ALA B 609 " ideal model delta sigma weight residual 1.454 1.485 -0.030 1.31e-02 5.83e+03 5.38e+00 bond pdb=" N ALA A 609 " pdb=" CA ALA A 609 " ideal model delta sigma weight residual 1.454 1.485 -0.030 1.31e-02 5.83e+03 5.34e+00 bond pdb=" CB TRP A 84 " pdb=" CG TRP A 84 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.15e+00 ... (remaining 9765 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.65: 165 104.65 - 112.10: 4704 112.10 - 119.55: 3499 119.55 - 127.01: 4765 127.01 - 134.46: 143 Bond angle restraints: 13276 Sorted by residual: angle pdb=" N SER A 390 " pdb=" CA SER A 390 " pdb=" C SER A 390 " ideal model delta sigma weight residual 111.28 100.90 10.38 1.09e+00 8.42e-01 9.07e+01 angle pdb=" N SER B 390 " pdb=" CA SER B 390 " pdb=" C SER B 390 " ideal model delta sigma weight residual 111.28 100.94 10.34 1.09e+00 8.42e-01 8.99e+01 angle pdb=" CA ALA A 609 " pdb=" C ALA A 609 " pdb=" N LEU A 610 " ideal model delta sigma weight residual 118.81 124.60 -5.79 1.15e+00 7.56e-01 2.54e+01 angle pdb=" CA ALA B 609 " pdb=" C ALA B 609 " pdb=" N LEU B 610 " ideal model delta sigma weight residual 118.81 124.60 -5.79 1.15e+00 7.56e-01 2.53e+01 angle pdb=" CA TYR B 352 " pdb=" CB TYR B 352 " pdb=" CG TYR B 352 " ideal model delta sigma weight residual 113.90 105.78 8.12 1.80e+00 3.09e-01 2.03e+01 ... (remaining 13271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 5204 13.97 - 27.94: 404 27.94 - 41.91: 114 41.91 - 55.88: 16 55.88 - 69.85: 2 Dihedral angle restraints: 5740 sinusoidal: 2266 harmonic: 3474 Sorted by residual: dihedral pdb=" CA TRP A 155 " pdb=" C TRP A 155 " pdb=" N SER A 156 " pdb=" CA SER A 156 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA TRP B 155 " pdb=" C TRP B 155 " pdb=" N SER B 156 " pdb=" CA SER B 156 " ideal model delta harmonic sigma weight residual 180.00 155.59 24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA LYS B 249 " pdb=" C LYS B 249 " pdb=" N ARG B 250 " pdb=" CA ARG B 250 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 5737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 871 0.047 - 0.094: 458 0.094 - 0.141: 138 0.141 - 0.188: 25 0.188 - 0.235: 12 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CA THR B 29 " pdb=" N THR B 29 " pdb=" C THR B 29 " pdb=" CB THR B 29 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR A 29 " pdb=" N THR A 29 " pdb=" C THR A 29 " pdb=" CB THR A 29 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA SER A 390 " pdb=" N SER A 390 " pdb=" C SER A 390 " pdb=" CB SER A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1501 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 352 " 0.040 2.00e-02 2.50e+03 2.14e-02 9.14e+00 pdb=" CG TYR A 352 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 352 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 352 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 352 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 352 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 352 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR A 352 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 352 " 0.040 2.00e-02 2.50e+03 2.13e-02 9.09e+00 pdb=" CG TYR B 352 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 352 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 352 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 352 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 352 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 352 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR B 352 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 376 " 0.045 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 377 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.038 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2596 2.79 - 3.32: 9281 3.32 - 3.84: 15371 3.84 - 4.37: 17589 4.37 - 4.90: 28764 Nonbonded interactions: 73601 Sorted by model distance: nonbonded pdb=" OH TYR A 212 " pdb=" OG SER A 526 " model vdw 2.262 2.440 nonbonded pdb=" OH TYR B 212 " pdb=" OG SER B 526 " model vdw 2.262 2.440 nonbonded pdb=" O VAL A 338 " pdb=" OG1 THR A 341 " model vdw 2.317 2.440 nonbonded pdb=" O ILE A 582 " pdb=" OG SER A 585 " model vdw 2.317 2.440 nonbonded pdb=" O ILE B 582 " pdb=" OG SER B 585 " model vdw 2.317 2.440 ... (remaining 73596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 38 5.16 5 C 6268 2.51 5 N 1572 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.000 Extract box with map and model: 4.730 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 28.190 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.009 0.078 9770 Z= 0.565 Angle : 1.156 10.379 13276 Z= 0.640 Chirality : 0.062 0.235 1504 Planarity : 0.008 0.066 1640 Dihedral : 11.245 69.847 3472 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.82 (0.17), residues: 1136 helix: -3.72 (0.11), residues: 754 sheet: -3.31 (1.18), residues: 22 loop : -3.72 (0.26), residues: 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 232 average time/residue: 0.2573 time to fit residues: 78.5882 Evaluate side-chains 99 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 230 GLN B 370 ASN B 499 ASN A 185 GLN A 230 GLN A 370 ASN A 499 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9770 Z= 0.222 Angle : 0.742 10.884 13276 Z= 0.383 Chirality : 0.043 0.192 1504 Planarity : 0.006 0.045 1640 Dihedral : 6.027 28.058 1284 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.21), residues: 1136 helix: -1.83 (0.15), residues: 790 sheet: -2.78 (1.09), residues: 22 loop : -3.57 (0.31), residues: 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.211 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 outliers start: 2 outliers final: 0 residues processed: 169 average time/residue: 0.1989 time to fit residues: 48.4112 Evaluate side-chains 96 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 518 GLN B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9770 Z= 0.236 Angle : 0.697 7.575 13276 Z= 0.355 Chirality : 0.044 0.150 1504 Planarity : 0.005 0.035 1640 Dihedral : 5.465 23.759 1284 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.23), residues: 1136 helix: -0.75 (0.17), residues: 776 sheet: -2.50 (1.04), residues: 22 loop : -3.38 (0.32), residues: 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.213 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2084 time to fit residues: 41.5501 Evaluate side-chains 103 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9770 Z= 0.166 Angle : 0.657 7.902 13276 Z= 0.326 Chirality : 0.042 0.142 1504 Planarity : 0.004 0.034 1640 Dihedral : 5.062 25.285 1284 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1136 helix: -0.20 (0.18), residues: 778 sheet: -1.82 (1.17), residues: 18 loop : -3.08 (0.31), residues: 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.171 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 outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1924 time to fit residues: 42.0181 Evaluate side-chains 95 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.0970 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9770 Z= 0.207 Angle : 0.680 7.754 13276 Z= 0.335 Chirality : 0.043 0.163 1504 Planarity : 0.004 0.031 1640 Dihedral : 4.874 20.891 1284 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.24), residues: 1136 helix: 0.12 (0.18), residues: 770 sheet: -1.60 (1.22), residues: 18 loop : -2.97 (0.31), residues: 348 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.225 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 outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1896 time to fit residues: 38.1844 Evaluate side-chains 91 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9770 Z= 0.204 Angle : 0.675 7.815 13276 Z= 0.333 Chirality : 0.043 0.159 1504 Planarity : 0.004 0.032 1640 Dihedral : 4.805 24.140 1284 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1136 helix: 0.24 (0.18), residues: 788 sheet: -1.55 (1.20), residues: 18 loop : -3.00 (0.31), residues: 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.253 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 outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1883 time to fit residues: 36.2996 Evaluate side-chains 92 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 148 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9770 Z= 0.178 Angle : 0.680 8.032 13276 Z= 0.331 Chirality : 0.042 0.141 1504 Planarity : 0.004 0.034 1640 Dihedral : 4.732 20.815 1284 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1136 helix: 0.44 (0.19), residues: 766 sheet: -1.46 (1.18), residues: 18 loop : -2.98 (0.30), residues: 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.194 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 outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1884 time to fit residues: 35.3437 Evaluate side-chains 89 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 148 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9770 Z= 0.185 Angle : 0.685 8.815 13276 Z= 0.334 Chirality : 0.043 0.187 1504 Planarity : 0.004 0.034 1640 Dihedral : 4.631 22.740 1284 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1136 helix: 0.53 (0.19), residues: 772 sheet: -1.45 (1.17), residues: 18 loop : -2.85 (0.31), residues: 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.522 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 outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1822 time to fit residues: 34.0955 Evaluate side-chains 86 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN A 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9770 Z= 0.193 Angle : 0.693 9.397 13276 Z= 0.335 Chirality : 0.043 0.144 1504 Planarity : 0.004 0.033 1640 Dihedral : 4.633 20.216 1284 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1136 helix: 0.61 (0.19), residues: 764 sheet: -1.57 (1.13), residues: 18 loop : -2.79 (0.31), residues: 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.223 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 outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1840 time to fit residues: 32.6494 Evaluate side-chains 85 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.0060 chunk 28 optimal weight: 0.0770 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN A 639 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9770 Z= 0.166 Angle : 0.685 9.927 13276 Z= 0.330 Chirality : 0.042 0.140 1504 Planarity : 0.004 0.035 1640 Dihedral : 4.515 22.266 1284 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1136 helix: 0.51 (0.19), residues: 778 sheet: -1.29 (1.20), residues: 18 loop : -2.68 (0.31), residues: 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1841 time to fit residues: 35.5906 Evaluate side-chains 89 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.0270 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 0.0670 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN ** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068956 restraints weight = 36620.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.070595 restraints weight = 20708.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071698 restraints weight = 13874.362| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9770 Z= 0.166 Angle : 0.683 9.635 13276 Z= 0.328 Chirality : 0.042 0.140 1504 Planarity : 0.004 0.034 1640 Dihedral : 4.462 21.821 1284 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1136 helix: 0.67 (0.19), residues: 782 sheet: -1.47 (1.14), residues: 18 loop : -2.61 (0.32), residues: 336 =============================================================================== Job complete usr+sys time: 1698.88 seconds wall clock time: 31 minutes 51.41 seconds (1911.41 seconds total)