Starting phenix.real_space_refine on Mon Mar 11 08:25:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9t_33691/03_2024/7y9t_33691.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9t_33691/03_2024/7y9t_33691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9t_33691/03_2024/7y9t_33691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9t_33691/03_2024/7y9t_33691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9t_33691/03_2024/7y9t_33691.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9t_33691/03_2024/7y9t_33691.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.122 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5054 2.51 5 N 1274 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 475": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7726 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2962 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 901 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 901 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "B" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2962 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.46, per 1000 atoms: 0.58 Number of scatterers: 7726 At special positions: 0 Unit cell: (125.4, 106.7, 95.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1342 8.00 N 1274 7.00 C 5054 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " distance=2.03 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: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 51.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 5 through 30 removed outlier: 3.575A pdb=" N HIS A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 13 " --> pdb=" O HIS A 9 " (cutoff:3.500A) Proline residue: A 16 - end of helix removed outlier: 3.686A pdb=" N ALA A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.759A pdb=" N SER A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.543A pdb=" N LEU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.791A pdb=" N LEU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.709A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.563A pdb=" N ILE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 128 through 143 removed outlier: 3.631A pdb=" N MET A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.543A pdb=" N LEU A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 152 " --> pdb=" O MET A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 165 removed outlier: 3.891A pdb=" N ILE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 460 through 471 removed outlier: 3.840A pdb=" N LEU A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 496 removed outlier: 3.612A pdb=" N ILE A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 4.754A pdb=" N LEU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 529 removed outlier: 3.684A pdb=" N MET A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.531A pdb=" N ALA A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.723A pdb=" N PHE A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 removed outlier: 3.715A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 558 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 573 removed outlier: 3.701A pdb=" N HIS A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 591 removed outlier: 3.541A pdb=" N VAL A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 removed outlier: 3.594A pdb=" N LEU A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 621 removed outlier: 3.884A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 30 removed outlier: 3.575A pdb=" N HIS B 9 " --> pdb=" O ALA B 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Proline residue: B 16 - end of helix removed outlier: 3.686A pdb=" N ALA B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.759A pdb=" N SER B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.543A pdb=" N LEU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 removed outlier: 3.791A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.709A pdb=" N LEU B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 104 removed outlier: 3.563A pdb=" N ILE B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 126 Processing helix chain 'B' and resid 128 through 143 removed outlier: 3.630A pdb=" N MET B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.544A pdb=" N LEU B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE B 152 " --> pdb=" O MET B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.891A pdb=" N ILE B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 460 through 471 removed outlier: 3.840A pdb=" N LEU B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 479 through 496 removed outlier: 3.612A pdb=" N ILE B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 512 removed outlier: 4.754A pdb=" N LEU B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 529 removed outlier: 3.685A pdb=" N MET B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.531A pdb=" N ALA B 541 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 549 removed outlier: 3.723A pdb=" N PHE B 548 " --> pdb=" O ALA B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 563 removed outlier: 3.715A pdb=" N VAL B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 558 " --> pdb=" O VAL B 554 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 removed outlier: 3.701A pdb=" N HIS B 570 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.541A pdb=" N VAL B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 608 removed outlier: 3.594A pdb=" N LEU B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 608 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 621 removed outlier: 3.884A pdb=" N LEU B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.860A pdb=" N ILE A 172 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL A 204 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER A 174 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 206 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS A 176 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 107 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 7 through 11 removed outlier: 3.522A pdb=" N GLN D 7 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 9 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER D 11 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 83 " --> pdb=" O CYS D 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 14 through 16 removed outlier: 5.430A pdb=" N GLY D 14 " --> pdb=" O THR D 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 removed outlier: 6.672A pdb=" N TRP D 40 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR D 41 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR D 99 " --> pdb=" O TYR D 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.663A pdb=" N TYR D 107 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE B 196 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG D 109 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE B 172 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 204 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER B 174 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL B 206 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS B 176 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.522A pdb=" N GLN C 7 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 9 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER C 11 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 83 " --> pdb=" O CYS C 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 16 removed outlier: 5.428A pdb=" N GLY C 14 " --> pdb=" O THR C 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.672A pdb=" N TRP C 40 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR C 41 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR C 99 " --> pdb=" O TYR C 41 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 747 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: 1.98 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.20: 78 1.20 - 1.36: 2361 1.36 - 1.51: 2924 1.51 - 1.66: 2447 1.66 - 1.81: 100 Bond restraints: 7910 Sorted by residual: bond pdb=" C ILE B 582 " pdb=" O ILE B 582 " ideal model delta sigma weight residual 1.236 1.054 0.182 1.19e-02 7.06e+03 2.35e+02 bond pdb=" C ILE A 582 " pdb=" O ILE A 582 " ideal model delta sigma weight residual 1.236 1.054 0.182 1.19e-02 7.06e+03 2.35e+02 bond pdb=" C THR A 146 " pdb=" O THR A 146 " ideal model delta sigma weight residual 1.236 1.088 0.148 1.31e-02 5.83e+03 1.27e+02 bond pdb=" C THR B 146 " pdb=" O THR B 146 " ideal model delta sigma weight residual 1.236 1.088 0.148 1.31e-02 5.83e+03 1.27e+02 bond pdb=" C ILE A 573 " pdb=" O ILE A 573 " ideal model delta sigma weight residual 1.239 1.112 0.127 1.13e-02 7.83e+03 1.26e+02 ... (remaining 7905 not shown) Histogram of bond angle deviations from ideal: 95.72 - 103.41: 154 103.41 - 111.10: 2925 111.10 - 118.79: 3248 118.79 - 126.48: 4246 126.48 - 134.16: 181 Bond angle restraints: 10754 Sorted by residual: angle pdb=" N LEU B 149 " pdb=" CA LEU B 149 " pdb=" C LEU B 149 " ideal model delta sigma weight residual 113.88 95.72 18.16 1.23e+00 6.61e-01 2.18e+02 angle pdb=" N LEU A 149 " pdb=" CA LEU A 149 " pdb=" C LEU A 149 " ideal model delta sigma weight residual 113.88 95.72 18.16 1.23e+00 6.61e-01 2.18e+02 angle pdb=" N ILE B 574 " pdb=" CA ILE B 574 " pdb=" C ILE B 574 " ideal model delta sigma weight residual 113.53 104.01 9.52 9.80e-01 1.04e+00 9.43e+01 angle pdb=" N ILE A 574 " pdb=" CA ILE A 574 " pdb=" C ILE A 574 " ideal model delta sigma weight residual 113.53 104.02 9.51 9.80e-01 1.04e+00 9.42e+01 angle pdb=" N TRP A 89 " pdb=" CA TRP A 89 " pdb=" C TRP A 89 " ideal model delta sigma weight residual 112.68 101.81 10.87 1.33e+00 5.65e-01 6.67e+01 ... (remaining 10749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 4340 15.19 - 30.38: 228 30.38 - 45.57: 82 45.57 - 60.77: 12 60.77 - 75.96: 4 Dihedral angle restraints: 4666 sinusoidal: 1792 harmonic: 2874 Sorted by residual: dihedral pdb=" N SER A 106 " pdb=" C SER A 106 " pdb=" CA SER A 106 " pdb=" CB SER A 106 " ideal model delta harmonic sigma weight residual 122.80 103.69 19.11 0 2.50e+00 1.60e-01 5.84e+01 dihedral pdb=" N SER B 106 " pdb=" C SER B 106 " pdb=" CA SER B 106 " pdb=" CB SER B 106 " ideal model delta harmonic sigma weight residual 122.80 103.74 19.06 0 2.50e+00 1.60e-01 5.81e+01 dihedral pdb=" CA GLN C 56 " pdb=" C GLN C 56 " pdb=" N SER C 57 " pdb=" CA SER C 57 " ideal model delta harmonic sigma weight residual 180.00 -143.98 -36.02 0 5.00e+00 4.00e-02 5.19e+01 ... (remaining 4663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1184 0.152 - 0.304: 52 0.304 - 0.455: 6 0.455 - 0.607: 6 0.607 - 0.759: 2 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CA SER A 27 " pdb=" N SER A 27 " pdb=" C SER A 27 " pdb=" CB SER A 27 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA SER B 27 " pdb=" N SER B 27 " pdb=" C SER B 27 " pdb=" CB SER B 27 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA HIS A 594 " pdb=" N HIS A 594 " pdb=" C HIS A 594 " pdb=" CB HIS A 594 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.73e+00 ... (remaining 1247 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 104 " 0.023 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C LEU A 104 " -0.076 2.00e-02 2.50e+03 pdb=" O LEU A 104 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE A 105 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 104 " -0.023 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C LEU B 104 " 0.076 2.00e-02 2.50e+03 pdb=" O LEU B 104 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE B 105 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 582 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ILE A 582 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE A 582 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL A 583 " 0.019 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2405 2.82 - 3.34: 6331 3.34 - 3.86: 11737 3.86 - 4.38: 13681 4.38 - 4.90: 24038 Nonbonded interactions: 58192 Sorted by model distance: nonbonded pdb=" NH2 ARG D 101 " pdb=" OE2 GLU B 191 " model vdw 2.305 2.520 nonbonded pdb=" OE2 GLU A 191 " pdb=" NH2 ARG C 101 " model vdw 2.334 2.520 nonbonded pdb=" ND2 ASN A 43 " pdb=" OG SER A 521 " model vdw 2.335 2.520 nonbonded pdb=" ND2 ASN B 43 " pdb=" OG SER B 521 " model vdw 2.335 2.520 nonbonded pdb=" N LEU B 149 " pdb=" N PHE B 150 " model vdw 2.362 2.560 ... (remaining 58187 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.630 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.018 0.182 7910 Z= 1.186 Angle : 1.561 18.157 10754 Z= 0.912 Chirality : 0.088 0.759 1250 Planarity : 0.010 0.077 1322 Dihedral : 11.121 75.956 2812 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.96 % Allowed : 4.57 % Favored : 94.47 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -6.23 (0.18), residues: 980 helix: -4.72 (0.08), residues: 522 sheet: -1.93 (0.49), residues: 126 loop : -3.58 (0.25), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP A 31 HIS 0.006 0.003 HIS A 594 PHE 0.024 0.004 PHE B 585 TYR 0.039 0.004 TYR B 617 ARG 0.005 0.001 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8572 (ttt) REVERT: A 201 LYS cc_start: 0.8452 (mmtp) cc_final: 0.8095 (mtpt) REVERT: A 208 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7187 (ttm-80) REVERT: A 468 MET cc_start: 0.8810 (mmm) cc_final: 0.8172 (mmm) REVERT: B 21 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8558 (ttt) REVERT: B 201 LYS cc_start: 0.8468 (mmtp) cc_final: 0.8102 (mtpt) REVERT: B 208 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7191 (ttm-80) REVERT: B 468 MET cc_start: 0.8819 (mmm) cc_final: 0.8207 (mmm) outliers start: 8 outliers final: 0 residues processed: 156 average time/residue: 0.2424 time to fit residues: 48.3829 Evaluate side-chains 97 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.0770 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 95 ASN A 164 GLN B 43 ASN B 95 ASN B 164 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7910 Z= 0.174 Angle : 0.593 6.916 10754 Z= 0.313 Chirality : 0.042 0.144 1250 Planarity : 0.007 0.051 1322 Dihedral : 5.165 31.391 1078 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.56 % Allowed : 8.05 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.86 (0.20), residues: 980 helix: -3.38 (0.15), residues: 528 sheet: -2.28 (0.47), residues: 116 loop : -2.89 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.004 0.001 HIS A 9 PHE 0.015 0.002 PHE A 585 TYR 0.011 0.001 TYR D 41 ARG 0.003 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 0.856 Fit side-chains REVERT: A 32 LYS cc_start: 0.8422 (mttp) cc_final: 0.8114 (mttm) REVERT: A 91 LYS cc_start: 0.8040 (tppt) cc_final: 0.7831 (mmtt) REVERT: A 124 MET cc_start: 0.8145 (mtp) cc_final: 0.7832 (mtp) REVERT: A 201 LYS cc_start: 0.8471 (mmtp) cc_final: 0.8107 (mtpt) REVERT: A 539 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7732 (mtt90) REVERT: C 51 TRP cc_start: 0.7578 (m-10) cc_final: 0.7306 (m-90) REVERT: B 32 LYS cc_start: 0.8493 (mttp) cc_final: 0.8136 (mttm) REVERT: B 91 LYS cc_start: 0.8134 (tppt) cc_final: 0.7928 (mmtt) REVERT: B 201 LYS cc_start: 0.8440 (mmtp) cc_final: 0.8092 (mtpt) REVERT: B 467 ILE cc_start: 0.8596 (mm) cc_final: 0.8354 (mm) REVERT: B 539 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7734 (mtt90) outliers start: 13 outliers final: 8 residues processed: 121 average time/residue: 0.2326 time to fit residues: 36.6787 Evaluate side-chains 100 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 0.0980 chunk 60 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7910 Z= 0.147 Angle : 0.523 6.932 10754 Z= 0.271 Chirality : 0.041 0.130 1250 Planarity : 0.005 0.047 1322 Dihedral : 4.596 29.512 1072 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.92 % Allowed : 8.89 % Favored : 89.18 % 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: -3.77 (0.23), residues: 980 helix: -2.35 (0.19), residues: 528 sheet: -1.94 (0.48), residues: 116 loop : -2.63 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 40 HIS 0.002 0.001 HIS A 9 PHE 0.010 0.001 PHE A 585 TYR 0.013 0.001 TYR D 41 ARG 0.002 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.883 Fit side-chains REVERT: A 124 MET cc_start: 0.8385 (mtp) cc_final: 0.7983 (mtp) REVERT: A 455 MET cc_start: 0.8549 (tpp) cc_final: 0.8341 (tpp) REVERT: A 467 ILE cc_start: 0.8610 (mm) cc_final: 0.8367 (mm) REVERT: B 91 LYS cc_start: 0.8025 (tppt) cc_final: 0.7800 (mmtt) REVERT: B 124 MET cc_start: 0.8391 (mtp) cc_final: 0.7969 (mtp) REVERT: B 201 LYS cc_start: 0.8378 (mmtp) cc_final: 0.7975 (mtpt) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.1642 time to fit residues: 26.1724 Evaluate side-chains 90 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 0.0020 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7910 Z= 0.151 Angle : 0.516 7.266 10754 Z= 0.266 Chirality : 0.041 0.137 1250 Planarity : 0.005 0.049 1322 Dihedral : 4.408 28.166 1072 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.92 % Allowed : 9.98 % Favored : 88.10 % 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: -3.12 (0.24), residues: 980 helix: -1.78 (0.21), residues: 526 sheet: -1.41 (0.53), residues: 92 loop : -2.48 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 40 HIS 0.002 0.001 HIS B 9 PHE 0.009 0.001 PHE A 585 TYR 0.014 0.001 TYR D 41 ARG 0.006 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.790 Fit side-chains REVERT: A 23 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8434 (tp) REVERT: A 124 MET cc_start: 0.8401 (mtp) cc_final: 0.8021 (mtp) REVERT: C 51 TRP cc_start: 0.7421 (m-90) cc_final: 0.7142 (m-90) REVERT: B 91 LYS cc_start: 0.7989 (tppt) cc_final: 0.7754 (mmtt) REVERT: B 124 MET cc_start: 0.8453 (mtp) cc_final: 0.8082 (mtp) REVERT: B 201 LYS cc_start: 0.8387 (mmtp) cc_final: 0.7942 (mtpt) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.1549 time to fit residues: 22.3549 Evaluate side-chains 93 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7910 Z= 0.185 Angle : 0.528 7.793 10754 Z= 0.268 Chirality : 0.042 0.136 1250 Planarity : 0.005 0.050 1322 Dihedral : 4.373 27.263 1072 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.92 % Allowed : 10.10 % Favored : 87.98 % 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: -2.78 (0.24), residues: 980 helix: -1.51 (0.22), residues: 524 sheet: -1.05 (0.55), residues: 86 loop : -2.37 (0.27), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 40 HIS 0.003 0.001 HIS B 9 PHE 0.018 0.002 PHE A 87 TYR 0.014 0.001 TYR D 41 ARG 0.004 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.844 Fit side-chains REVERT: A 23 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8487 (tp) REVERT: A 124 MET cc_start: 0.8531 (mtp) cc_final: 0.8164 (mtp) REVERT: C 51 TRP cc_start: 0.7416 (m-90) cc_final: 0.7156 (m-90) REVERT: B 23 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8435 (tp) REVERT: B 91 LYS cc_start: 0.7977 (tppt) cc_final: 0.7749 (mmtt) REVERT: B 124 MET cc_start: 0.8583 (mtp) cc_final: 0.8213 (mtp) REVERT: B 201 LYS cc_start: 0.8399 (mmtp) cc_final: 0.7920 (mtpt) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.1491 time to fit residues: 21.9895 Evaluate side-chains 97 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7910 Z= 0.160 Angle : 0.507 7.501 10754 Z= 0.258 Chirality : 0.041 0.132 1250 Planarity : 0.005 0.050 1322 Dihedral : 4.250 26.952 1072 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.52 % Allowed : 10.58 % Favored : 86.90 % 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: -2.36 (0.25), residues: 980 helix: -1.13 (0.22), residues: 520 sheet: -1.06 (0.53), residues: 86 loop : -2.17 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 40 HIS 0.002 0.000 HIS B 9 PHE 0.014 0.001 PHE A 87 TYR 0.014 0.001 TYR D 41 ARG 0.004 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.856 Fit side-chains REVERT: A 23 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8422 (tp) REVERT: A 124 MET cc_start: 0.8555 (mtp) cc_final: 0.8165 (mtp) REVERT: C 51 TRP cc_start: 0.7458 (m-90) cc_final: 0.7192 (m-90) REVERT: B 23 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8425 (tp) REVERT: B 124 MET cc_start: 0.8570 (mtp) cc_final: 0.8206 (mtp) REVERT: B 201 LYS cc_start: 0.8446 (mmtp) cc_final: 0.7972 (mtpt) outliers start: 21 outliers final: 15 residues processed: 100 average time/residue: 0.1505 time to fit residues: 22.3633 Evaluate side-chains 100 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7910 Z= 0.294 Angle : 0.583 8.130 10754 Z= 0.293 Chirality : 0.044 0.126 1250 Planarity : 0.005 0.050 1322 Dihedral : 4.499 27.030 1072 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.76 % Allowed : 10.70 % Favored : 86.54 % 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: -2.52 (0.24), residues: 980 helix: -1.26 (0.21), residues: 528 sheet: -1.15 (0.52), residues: 86 loop : -2.25 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 37 HIS 0.004 0.001 HIS B 9 PHE 0.015 0.002 PHE A 87 TYR 0.015 0.002 TYR D 41 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.849 Fit side-chains REVERT: A 23 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 124 MET cc_start: 0.8564 (mtp) cc_final: 0.8178 (mtp) REVERT: A 201 LYS cc_start: 0.8391 (mmtp) cc_final: 0.7826 (mtpt) REVERT: C 51 TRP cc_start: 0.7421 (m-90) cc_final: 0.7169 (m-90) REVERT: B 23 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8535 (tp) REVERT: B 124 MET cc_start: 0.8601 (mtp) cc_final: 0.8242 (mtp) REVERT: B 201 LYS cc_start: 0.8281 (mmtp) cc_final: 0.7892 (mtpt) outliers start: 23 outliers final: 17 residues processed: 103 average time/residue: 0.1583 time to fit residues: 23.8688 Evaluate side-chains 106 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7910 Z= 0.146 Angle : 0.506 7.828 10754 Z= 0.256 Chirality : 0.041 0.124 1250 Planarity : 0.005 0.051 1322 Dihedral : 4.256 26.613 1072 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.16 % Allowed : 11.06 % Favored : 86.78 % 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: -2.00 (0.25), residues: 980 helix: -0.77 (0.22), residues: 520 sheet: -1.08 (0.51), residues: 86 loop : -2.05 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 40 HIS 0.002 0.000 HIS B 9 PHE 0.013 0.001 PHE A 87 TYR 0.014 0.001 TYR D 41 ARG 0.004 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.872 Fit side-chains REVERT: A 124 MET cc_start: 0.8546 (mtp) cc_final: 0.8183 (mtp) REVERT: A 133 MET cc_start: 0.8931 (mmm) cc_final: 0.8717 (mmp) REVERT: C 51 TRP cc_start: 0.7394 (m-90) cc_final: 0.7142 (m-90) REVERT: B 124 MET cc_start: 0.8582 (mtp) cc_final: 0.8202 (mtp) REVERT: B 201 LYS cc_start: 0.8364 (mmtp) cc_final: 0.7854 (mtpt) outliers start: 18 outliers final: 15 residues processed: 99 average time/residue: 0.1517 time to fit residues: 22.3670 Evaluate side-chains 93 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 TRP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7910 Z= 0.166 Angle : 0.513 7.989 10754 Z= 0.258 Chirality : 0.041 0.126 1250 Planarity : 0.005 0.051 1322 Dihedral : 4.171 25.816 1072 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.16 % Allowed : 11.78 % Favored : 86.06 % 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: -1.76 (0.25), residues: 980 helix: -0.54 (0.23), residues: 520 sheet: -1.03 (0.51), residues: 86 loop : -1.99 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 37 HIS 0.002 0.001 HIS A 9 PHE 0.013 0.001 PHE A 87 TYR 0.013 0.001 TYR C 41 ARG 0.003 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.967 Fit side-chains REVERT: A 124 MET cc_start: 0.8563 (mtp) cc_final: 0.8194 (mtp) REVERT: A 133 MET cc_start: 0.8941 (mmm) cc_final: 0.8740 (mmp) REVERT: C 51 TRP cc_start: 0.7359 (m-90) cc_final: 0.7130 (m-90) REVERT: B 124 MET cc_start: 0.8546 (mtp) cc_final: 0.8185 (mtp) REVERT: B 201 LYS cc_start: 0.8220 (mmtp) cc_final: 0.7845 (mtpt) outliers start: 18 outliers final: 16 residues processed: 98 average time/residue: 0.1571 time to fit residues: 23.0288 Evaluate side-chains 96 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 37 TRP Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 TRP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 0.0170 chunk 47 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7910 Z= 0.173 Angle : 0.513 8.082 10754 Z= 0.258 Chirality : 0.042 0.125 1250 Planarity : 0.005 0.051 1322 Dihedral : 4.156 25.627 1072 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.04 % Allowed : 12.26 % Favored : 85.70 % 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: -1.63 (0.25), residues: 980 helix: -0.42 (0.23), residues: 520 sheet: -0.92 (0.52), residues: 86 loop : -1.97 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 37 HIS 0.002 0.001 HIS A 9 PHE 0.013 0.001 PHE A 87 TYR 0.013 0.001 TYR C 41 ARG 0.004 0.000 ARG A 539 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.959 Fit side-chains REVERT: A 124 MET cc_start: 0.8572 (mtp) cc_final: 0.8264 (mtp) REVERT: B 124 MET cc_start: 0.8545 (mtp) cc_final: 0.8175 (mtp) REVERT: B 201 LYS cc_start: 0.8267 (mmtp) cc_final: 0.7879 (mtpt) REVERT: B 555 MET cc_start: 0.8928 (tpp) cc_final: 0.8601 (tpp) outliers start: 17 outliers final: 15 residues processed: 96 average time/residue: 0.1559 time to fit residues: 22.5718 Evaluate side-chains 96 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 37 TRP Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 37 TRP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.158629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104786 restraints weight = 8999.508| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.82 r_work: 0.2826 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7910 Z= 0.123 Angle : 0.488 7.722 10754 Z= 0.245 Chirality : 0.041 0.130 1250 Planarity : 0.005 0.051 1322 Dihedral : 3.974 24.245 1072 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.92 % Allowed : 12.62 % Favored : 85.46 % 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: -1.38 (0.26), residues: 980 helix: -0.17 (0.23), residues: 520 sheet: -0.80 (0.52), residues: 86 loop : -1.93 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 40 HIS 0.001 0.000 HIS B 9 PHE 0.021 0.001 PHE B 87 TYR 0.013 0.001 TYR D 41 ARG 0.004 0.000 ARG A 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.72 seconds wall clock time: 34 minutes 14.40 seconds (2054.40 seconds total)