Starting phenix.real_space_refine on Sat Dec 28 04:05:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y9t_33691/12_2024/7y9t_33691.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y9t_33691/12_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/cci-nas-00/data/ceres_data/7y9t_33691/12_2024/7y9t_33691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y9t_33691/12_2024/7y9t_33691.map" model { file = "/net/cci-nas-00/data/ceres_data/7y9t_33691/12_2024/7y9t_33691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y9t_33691/12_2024/7y9t_33691.cif" } 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. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7726 Number of models: 1 Model: "" Number of chains: 2 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: "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} Restraints were copied for chains: B, D Time building chain proxies: 5.73, per 1000 atoms: 0.74 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.1 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: 0.84 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: 1.88 Time building geometry restraints manager: 2.05 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: 0.00 - 3.63: 10368 3.63 - 7.26: 302 7.26 - 10.89: 62 10.89 - 14.53: 18 14.53 - 18.16: 4 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: 4339 15.19 - 30.38: 227 30.38 - 45.57: 81 45.57 - 60.77: 12 60.77 - 75.96: 4 Dihedral angle restraints: 4663 sinusoidal: 1789 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 4660 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: 2.03 - 2.61: 101 2.61 - 3.18: 5935 3.18 - 3.75: 10939 3.75 - 4.33: 15320 4.33 - 4.90: 25900 Nonbonded interactions: 58195 Sorted by model distance: nonbonded pdb=" SG CYS C 26 " pdb=" SG CYS C 100 " model vdw 2.034 3.760 nonbonded pdb=" NH2 ARG D 101 " pdb=" OE2 GLU B 191 " model vdw 2.305 3.120 nonbonded pdb=" OE2 GLU A 191 " pdb=" NH2 ARG C 101 " model vdw 2.334 3.120 nonbonded pdb=" ND2 ASN A 43 " pdb=" OG SER A 521 " model vdw 2.335 3.120 nonbonded pdb=" ND2 ASN B 43 " pdb=" OG SER B 521 " model vdw 2.335 3.120 ... (remaining 58190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.130 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- 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= 1.201 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 : 2.034 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 to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.810 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: 0.2431 time to fit residues: 48.9288 Evaluate side-chains 97 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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: 0.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.0060 chunk 39 optimal weight: 0.0060 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 164 GLN B 95 ASN B 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7910 Z= 0.157 Angle : 0.596 6.498 10754 Z= 0.315 Chirality : 0.042 0.142 1250 Planarity : 0.007 0.048 1322 Dihedral : 5.100 31.218 1078 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.56 % Allowed : 8.17 % Favored : 90.26 % 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: -4.85 (0.20), residues: 980 helix: -3.36 (0.15), residues: 528 sheet: -2.36 (0.46), residues: 116 loop : -2.88 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 37 HIS 0.004 0.001 HIS A 9 PHE 0.014 0.001 PHE A 585 TYR 0.010 0.001 TYR D 41 ARG 0.003 0.000 ARG B 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 130 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.881 Fit side-chains REVERT: A 32 LYS cc_start: 0.8481 (mttp) cc_final: 0.8183 (mttm) REVERT: A 201 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8093 (mtpt) REVERT: A 539 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7720 (mtt90) REVERT: D 38 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7840 (mtp) REVERT: C 51 TRP cc_start: 0.7575 (m-10) cc_final: 0.7318 (m-90) REVERT: B 32 LYS cc_start: 0.8547 (mttp) cc_final: 0.8176 (mttm) REVERT: B 201 LYS cc_start: 0.8431 (mmtp) cc_final: 0.8092 (mtpt) REVERT: B 539 ARG cc_start: 0.8024 (mtt-85) cc_final: 0.7743 (mtt90) outliers start: 13 outliers final: 5 residues processed: 124 average time/residue: 0.2356 time to fit residues: 38.3387 Evaluate side-chains 98 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 38 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2534 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 : 0.550 7.132 10754 Z= 0.285 Chirality : 0.042 0.136 1250 Planarity : 0.005 0.048 1322 Dihedral : 4.625 29.031 1072 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.16 % Allowed : 9.86 % 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: -3.71 (0.23), residues: 980 helix: -2.32 (0.19), residues: 524 sheet: -1.76 (0.49), residues: 110 loop : -2.63 (0.26), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 40 HIS 0.003 0.001 HIS A 9 PHE 0.011 0.002 PHE A 585 TYR 0.013 0.001 TYR D 41 ARG 0.002 0.000 ARG C 109 *********************** 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 114 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.878 Fit side-chains REVERT: A 23 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 201 LYS cc_start: 0.8412 (mmtp) cc_final: 0.7992 (mtpt) REVERT: A 455 MET cc_start: 0.8566 (tpp) cc_final: 0.8298 (tpp) REVERT: A 467 ILE cc_start: 0.8605 (mm) cc_final: 0.8370 (mm) REVERT: B 23 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8438 (tp) REVERT: B 124 MET cc_start: 0.8350 (mtp) cc_final: 0.7987 (mtp) REVERT: B 201 LYS cc_start: 0.8379 (mmtp) cc_final: 0.7974 (mtpt) REVERT: B 455 MET cc_start: 0.8582 (tpp) cc_final: 0.8342 (tpp) REVERT: B 467 ILE cc_start: 0.8610 (mm) cc_final: 0.8401 (mm) outliers start: 18 outliers final: 9 residues processed: 110 average time/residue: 0.1875 time to fit residues: 28.7372 Evaluate side-chains 91 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 205 THR 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 184 LEU Chi-restraints excluded: chain B residue 205 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8372 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7910 Z= 0.233 Angle : 0.567 7.454 10754 Z= 0.292 Chirality : 0.043 0.132 1250 Planarity : 0.005 0.052 1322 Dihedral : 4.587 28.217 1072 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.40 % Allowed : 10.10 % Favored : 87.50 % 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: -3.19 (0.23), residues: 980 helix: -1.91 (0.21), residues: 518 sheet: -1.27 (0.54), residues: 86 loop : -2.43 (0.26), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 37 HIS 0.003 0.001 HIS B 9 PHE 0.012 0.002 PHE B 585 TYR 0.014 0.001 TYR A 617 ARG 0.006 0.001 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 110 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 467 ILE cc_start: 0.8649 (mm) cc_final: 0.8394 (mm) REVERT: B 23 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8479 (tp) REVERT: B 124 MET cc_start: 0.8484 (mtp) cc_final: 0.8106 (mtp) REVERT: B 201 LYS cc_start: 0.8404 (mmtp) cc_final: 0.7936 (mtpt) REVERT: B 467 ILE cc_start: 0.8650 (mm) cc_final: 0.8438 (mm) outliers start: 20 outliers final: 14 residues processed: 102 average time/residue: 0.1755 time to fit residues: 25.8315 Evaluate side-chains 94 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 95 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 205 THR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.0270 overall best weight: 0.7438 ------------------------------------------------------------------------------- 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: 0.8356 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7910 Z= 0.170 Angle : 0.524 7.505 10754 Z= 0.269 Chirality : 0.042 0.132 1250 Planarity : 0.005 0.051 1322 Dihedral : 4.411 26.881 1072 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.80 % Allowed : 10.82 % Favored : 87.38 % 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: -2.69 (0.24), residues: 980 helix: -1.44 (0.22), residues: 518 sheet: -1.16 (0.53), residues: 86 loop : -2.27 (0.27), residues: 376 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 0.017 0.002 PHE A 87 TYR 0.014 0.001 TYR D 41 ARG 0.005 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 104 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.940 Fit side-chains REVERT: A 23 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8411 (tp) REVERT: A 467 ILE cc_start: 0.8592 (mm) cc_final: 0.8365 (mm) REVERT: B 124 MET cc_start: 0.8541 (mtp) cc_final: 0.8167 (mtp) REVERT: B 201 LYS cc_start: 0.8394 (mmtp) cc_final: 0.7887 (mtpt) REVERT: B 467 ILE cc_start: 0.8657 (mm) cc_final: 0.8441 (mm) outliers start: 15 outliers final: 14 residues processed: 98 average time/residue: 0.1539 time to fit residues: 22.5235 Evaluate side-chains 98 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 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 92 LEU Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 205 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 88 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 55 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7910 Z= 0.132 Angle : 0.499 7.575 10754 Z= 0.255 Chirality : 0.041 0.132 1250 Planarity : 0.005 0.050 1322 Dihedral : 4.203 26.343 1072 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.68 % Allowed : 11.78 % 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: -2.20 (0.25), residues: 980 helix: -0.97 (0.22), residues: 518 sheet: -0.99 (0.53), residues: 86 loop : -2.13 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 40 HIS 0.001 0.000 HIS A 9 PHE 0.014 0.001 PHE A 87 TYR 0.018 0.001 TYR D 41 ARG 0.004 0.000 ARG A 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 109 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.870 Fit side-chains REVERT: A 23 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 467 ILE cc_start: 0.8624 (mm) cc_final: 0.8391 (mm) REVERT: C 51 TRP cc_start: 0.7408 (m-90) cc_final: 0.7165 (m-90) REVERT: C 87 MET cc_start: 0.5579 (mmp) cc_final: 0.5219 (tpt) REVERT: B 124 MET cc_start: 0.8568 (mtp) cc_final: 0.8227 (mtp) REVERT: B 201 LYS cc_start: 0.8404 (mmtp) cc_final: 0.7919 (mtpt) REVERT: B 467 ILE cc_start: 0.8610 (mm) cc_final: 0.8397 (mm) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 0.1466 time to fit residues: 22.9707 Evaluate side-chains 103 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 205 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 88 LEU Chi-restraints excluded: chain B residue 205 THR 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: 4.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7910 Z= 0.279 Angle : 0.576 7.991 10754 Z= 0.291 Chirality : 0.044 0.124 1250 Planarity : 0.005 0.051 1322 Dihedral : 4.423 25.996 1072 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.92 % Allowed : 11.78 % Favored : 86.30 % 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: -2.20 (0.25), residues: 980 helix: -1.02 (0.22), residues: 524 sheet: -0.92 (0.53), residues: 86 loop : -2.08 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 37 HIS 0.003 0.001 HIS A 9 PHE 0.015 0.002 PHE A 87 TYR 0.022 0.002 TYR A 617 ARG 0.002 0.000 ARG A 155 *********************** 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 113 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.907 Fit side-chains REVERT: A 23 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8499 (tp) REVERT: A 201 LYS cc_start: 0.8388 (mmtp) cc_final: 0.7820 (mtpt) REVERT: C 87 MET cc_start: 0.5535 (mmp) cc_final: 0.5262 (tpt) REVERT: B 124 MET cc_start: 0.8623 (mtp) cc_final: 0.8210 (mtp) REVERT: B 201 LYS cc_start: 0.8397 (mmtp) cc_final: 0.7883 (mtpt) outliers start: 16 outliers final: 14 residues processed: 107 average time/residue: 0.1612 time to fit residues: 25.1997 Evaluate side-chains 112 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 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 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 613 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8362 moved from start: 0.3270 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= 0.171 Angle : 0.519 7.792 10754 Z= 0.263 Chirality : 0.042 0.122 1250 Planarity : 0.005 0.051 1322 Dihedral : 4.264 25.526 1072 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.92 % Allowed : 11.90 % Favored : 86.18 % 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: -1.88 (0.25), residues: 980 helix: -0.68 (0.22), residues: 514 sheet: -0.89 (0.52), residues: 86 loop : -2.01 (0.28), residues: 380 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 0.016 0.001 TYR A 617 ARG 0.004 0.000 ARG B 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 115 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.755 Fit side-chains REVERT: A 23 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8401 (tp) REVERT: C 87 MET cc_start: 0.5657 (mmp) cc_final: 0.5384 (tpt) REVERT: B 124 MET cc_start: 0.8615 (mtp) cc_final: 0.8297 (mtp) REVERT: B 201 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7847 (mtpt) outliers start: 16 outliers final: 11 residues processed: 110 average time/residue: 0.1820 time to fit residues: 28.1383 Evaluate side-chains 101 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 205 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.8378 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7910 Z= 0.206 Angle : 0.540 8.234 10754 Z= 0.272 Chirality : 0.042 0.123 1250 Planarity : 0.005 0.052 1322 Dihedral : 4.283 24.692 1072 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.68 % Allowed : 12.74 % Favored : 85.58 % 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: -1.75 (0.25), residues: 980 helix: -0.56 (0.22), residues: 514 sheet: -0.87 (0.52), residues: 86 loop : -1.96 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 37 HIS 0.003 0.001 HIS A 9 PHE 0.013 0.002 PHE A 87 TYR 0.014 0.001 TYR D 41 ARG 0.003 0.000 ARG B 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 105 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.816 Fit side-chains REVERT: A 23 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8457 (tp) REVERT: A 201 LYS cc_start: 0.8344 (mmtp) cc_final: 0.7954 (mtpt) REVERT: C 87 MET cc_start: 0.5632 (mmp) cc_final: 0.5390 (tpt) REVERT: B 124 MET cc_start: 0.8609 (mtp) cc_final: 0.8284 (mtp) REVERT: B 201 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7906 (mtpt) outliers start: 14 outliers final: 12 residues processed: 102 average time/residue: 0.1660 time to fit residues: 24.7808 Evaluate side-chains 103 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 205 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 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 613 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.0020 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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: 0.8349 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7910 Z= 0.143 Angle : 0.509 7.723 10754 Z= 0.256 Chirality : 0.041 0.122 1250 Planarity : 0.005 0.052 1322 Dihedral : 4.123 23.991 1072 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.44 % Allowed : 13.22 % Favored : 85.34 % 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: -1.40 (0.26), residues: 980 helix: -0.24 (0.23), residues: 514 sheet: -0.74 (0.52), residues: 86 loop : -1.86 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 37 HIS 0.002 0.000 HIS A 9 PHE 0.012 0.001 PHE B 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 103 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.919 Fit side-chains REVERT: A 201 LYS cc_start: 0.8453 (mmtp) cc_final: 0.7923 (mtpt) REVERT: C 87 MET cc_start: 0.5588 (mmp) cc_final: 0.5382 (tpt) REVERT: B 124 MET cc_start: 0.8569 (mtp) cc_final: 0.8246 (mtp) REVERT: B 201 LYS cc_start: 0.8257 (mmtp) cc_final: 0.7871 (mtpt) outliers start: 12 outliers final: 10 residues processed: 100 average time/residue: 0.1735 time to fit residues: 25.4400 Evaluate side-chains 99 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 205 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.0010 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.166316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115486 restraints weight = 8823.275| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.76 r_work: 0.2832 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7910 Z= 0.138 Angle : 0.508 7.855 10754 Z= 0.253 Chirality : 0.041 0.124 1250 Planarity : 0.005 0.051 1322 Dihedral : 4.017 22.660 1072 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.56 % Allowed : 12.98 % 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: -1.13 (0.26), residues: 980 helix: 0.00 (0.23), residues: 514 sheet: -0.58 (0.52), residues: 86 loop : -1.77 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 40 HIS 0.002 0.000 HIS A 9 PHE 0.012 0.001 PHE B 87 TYR 0.014 0.001 TYR C 41 ARG 0.004 0.000 ARG B 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.91 seconds wall clock time: 34 minutes 53.70 seconds (2093.70 seconds total)