Starting phenix.real_space_refine on Tue Jun 17 04:44:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnl_26013/06_2025/7tnl_26013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnl_26013/06_2025/7tnl_26013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnl_26013/06_2025/7tnl_26013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnl_26013/06_2025/7tnl_26013.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnl_26013/06_2025/7tnl_26013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnl_26013/06_2025/7tnl_26013.cif" } resolution = 3.59 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12558 2.51 5 N 3144 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19434 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4828 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4828 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.90, per 1000 atoms: 0.56 Number of scatterers: 19434 At special positions: 0 Unit cell: (123.67, 115.37, 131.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3592 8.00 N 3144 7.00 C 12558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.04 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.01 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.04 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.04 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.01 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.02 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: 4.43 Conformation dependent library (CDL) restraints added in 2.4 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 22 sheets defined 55.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.870A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 524 through 545 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 removed outlier: 3.583A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.638A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.511A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 677 removed outlier: 3.666A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.607A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 769 removed outlier: 3.725A pdb=" N TYR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 removed outlier: 4.008A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1029 Processing helix chain 'A' and resid 1050 through 1054 removed outlier: 3.828A pdb=" N ASN A1053 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1104 Processing helix chain 'A' and resid 1104 through 1126 removed outlier: 4.661A pdb=" N GLU A1125 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE A1126 " --> pdb=" O ALA A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1159 removed outlier: 3.542A pdb=" N VAL A1154 " --> pdb=" O ILE A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1209 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.594A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 545 removed outlier: 3.527A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.607A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 617 removed outlier: 3.739A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 625 removed outlier: 3.597A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.612A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 774 through 781 removed outlier: 3.596A pdb=" N SER B 778 " --> pdb=" O GLY B 774 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.832A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1029 Processing helix chain 'B' and resid 1091 through 1104 Processing helix chain 'B' and resid 1104 through 1126 removed outlier: 3.543A pdb=" N LEU B1114 " --> pdb=" O SER B1110 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE B1126 " --> pdb=" O ALA B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1159 removed outlier: 3.515A pdb=" N ILE B1150 " --> pdb=" O LEU B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1209 removed outlier: 3.513A pdb=" N TYR B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B1204 " --> pdb=" O PHE B1200 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.870A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 524 through 545 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 removed outlier: 3.583A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.638A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.511A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 removed outlier: 3.665A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.607A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 769 removed outlier: 3.725A pdb=" N TYR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 820 removed outlier: 4.008A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1029 Processing helix chain 'C' and resid 1050 through 1054 removed outlier: 3.828A pdb=" N ASN C1053 " --> pdb=" O SER C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1104 Processing helix chain 'C' and resid 1104 through 1126 removed outlier: 4.660A pdb=" N GLU C1125 " --> pdb=" O ILE C1121 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C1126 " --> pdb=" O ALA C1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1159 removed outlier: 3.543A pdb=" N VAL C1154 " --> pdb=" O ILE C1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 1176 through 1209 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.596A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 removed outlier: 3.528A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.607A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 617 removed outlier: 3.740A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 625 removed outlier: 3.598A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.613A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 774 through 781 removed outlier: 3.597A pdb=" N SER D 778 " --> pdb=" O GLY D 774 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.832A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1029 Processing helix chain 'D' and resid 1091 through 1104 Processing helix chain 'D' and resid 1104 through 1126 removed outlier: 3.542A pdb=" N LEU D1114 " --> pdb=" O SER D1110 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE D1126 " --> pdb=" O ALA D1122 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1159 removed outlier: 3.515A pdb=" N ILE D1150 " --> pdb=" O LEU D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1209 removed outlier: 3.513A pdb=" N TYR D1180 " --> pdb=" O GLY D1176 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS D1204 " --> pdb=" O PHE D1200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 498 removed outlier: 5.075A pdb=" N ILE A 734 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A 732 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N MET A 496 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS A 730 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.539A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 3.698A pdb=" N LYS A1077 " --> pdb=" O THR A1065 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.251A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.652A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.776A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 3.869A pdb=" N VAL B1056 " --> pdb=" O GLY B1037 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B1033 " --> pdb=" O SER B1060 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 489 through 498 removed outlier: 5.074A pdb=" N ILE C 734 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR C 732 " --> pdb=" O PRO C 494 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N MET C 496 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS C 730 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.539A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1076 through 1078 removed outlier: 3.698A pdb=" N LYS C1077 " --> pdb=" O THR C1065 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.251A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC2, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.652A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.777A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1076 through 1078 removed outlier: 3.869A pdb=" N VAL D1056 " --> pdb=" O GLY D1037 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D1033 " --> pdb=" O SER D1060 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 3138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.07 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5667 1.34 - 1.46: 3896 1.46 - 1.57: 10075 1.57 - 1.69: 8 1.69 - 1.81: 220 Bond restraints: 19866 Sorted by residual: bond pdb=" CB ILE A 525 " pdb=" CG2 ILE A 525 " ideal model delta sigma weight residual 1.521 1.389 0.132 3.30e-02 9.18e+02 1.60e+01 bond pdb=" CB ILE C 525 " pdb=" CG2 ILE C 525 " ideal model delta sigma weight residual 1.521 1.390 0.131 3.30e-02 9.18e+02 1.58e+01 bond pdb=" N GLU A1046 " pdb=" CA GLU A1046 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.17e-02 7.31e+03 8.13e+00 bond pdb=" N GLU C1046 " pdb=" CA GLU C1046 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.17e-02 7.31e+03 7.98e+00 bond pdb=" CG1 ILE C 525 " pdb=" CD1 ILE C 525 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.16e+00 ... (remaining 19861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 25858 2.38 - 4.77: 815 4.77 - 7.15: 131 7.15 - 9.54: 30 9.54 - 11.92: 8 Bond angle restraints: 26842 Sorted by residual: angle pdb=" C GLU D1054 " pdb=" N GLU D1055 " pdb=" CA GLU D1055 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C GLU B1054 " pdb=" N GLU B1055 " pdb=" CA GLU B1055 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C SER B1045 " pdb=" N GLU B1046 " pdb=" CA GLU B1046 " ideal model delta sigma weight residual 121.19 130.84 -9.65 1.59e+00 3.96e-01 3.68e+01 angle pdb=" C SER D1045 " pdb=" N GLU D1046 " pdb=" CA GLU D1046 " ideal model delta sigma weight residual 121.19 130.82 -9.63 1.59e+00 3.96e-01 3.67e+01 angle pdb=" C SER C1045 " pdb=" N GLU C1046 " pdb=" CA GLU C1046 " ideal model delta sigma weight residual 121.19 130.03 -8.84 1.59e+00 3.96e-01 3.09e+01 ... (remaining 26837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 11406 24.11 - 48.23: 346 48.23 - 72.34: 28 72.34 - 96.45: 6 96.45 - 120.57: 10 Dihedral angle restraints: 11796 sinusoidal: 4666 harmonic: 7130 Sorted by residual: dihedral pdb=" CA GLU A 627 " pdb=" C GLU A 627 " pdb=" N ARG A 628 " pdb=" CA ARG A 628 " ideal model delta harmonic sigma weight residual 180.00 138.84 41.16 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA GLU C 627 " pdb=" C GLU C 627 " pdb=" N ARG C 628 " pdb=" CA ARG C 628 " ideal model delta harmonic sigma weight residual 180.00 138.85 41.15 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA GLU B1054 " pdb=" C GLU B1054 " pdb=" N GLU B1055 " pdb=" CA GLU B1055 " ideal model delta harmonic sigma weight residual 180.00 142.19 37.81 0 5.00e+00 4.00e-02 5.72e+01 ... (remaining 11793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2471 0.071 - 0.143: 440 0.143 - 0.214: 71 0.214 - 0.285: 14 0.285 - 0.356: 2 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU A1114 " pdb=" CB LEU A1114 " pdb=" CD1 LEU A1114 " pdb=" CD2 LEU A1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CG LEU C1114 " pdb=" CB LEU C1114 " pdb=" CD1 LEU C1114 " pdb=" CD2 LEU C1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB THR C1065 " pdb=" CA THR C1065 " pdb=" OG1 THR C1065 " pdb=" CG2 THR C1065 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2995 not shown) Planarity restraints: 3312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 627 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C GLU C 627 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU C 627 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG C 628 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 627 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C GLU A 627 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 627 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 628 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO C 520 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.032 5.00e-02 4.00e+02 ... (remaining 3309 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4701 2.78 - 3.31: 17964 3.31 - 3.84: 31508 3.84 - 4.37: 37019 4.37 - 4.90: 64299 Nonbonded interactions: 155491 Sorted by model distance: nonbonded pdb=" OD1 ASP C1047 " pdb=" OG SER C1050 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP A1047 " pdb=" OG SER A1050 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR C 655 " pdb=" OE2 GLU C 705 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR A 655 " pdb=" OE2 GLU A 705 " model vdw 2.282 3.040 nonbonded pdb=" OG SER A 597 " pdb=" O ALA B 806 " model vdw 2.315 3.040 ... (remaining 155486 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 41.970 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.132 19878 Z= 0.385 Angle : 1.030 11.924 26866 Z= 0.556 Chirality : 0.059 0.356 2998 Planarity : 0.007 0.057 3312 Dihedral : 11.859 120.568 7212 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.12 % Rotamer: Outliers : 0.38 % Allowed : 5.75 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.39 (0.12), residues: 2460 helix: -3.43 (0.07), residues: 1320 sheet: -1.45 (0.35), residues: 168 loop : -2.12 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP A 671 HIS 0.007 0.003 HIS A1131 PHE 0.038 0.003 PHE C 623 TYR 0.028 0.003 TYR D 702 ARG 0.012 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.27055 ( 1078) hydrogen bonds : angle 8.99511 ( 3138) SS BOND : bond 0.01176 ( 12) SS BOND : angle 1.90627 ( 24) covalent geometry : bond 0.00921 (19866) covalent geometry : angle 1.02879 (26842) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 554 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7602 (mpt) cc_final: 0.7376 (mtp) REVERT: A 668 ASP cc_start: 0.7611 (t70) cc_final: 0.7335 (t0) REVERT: A 695 LYS cc_start: 0.8648 (mptt) cc_final: 0.8349 (pttp) REVERT: A 817 LYS cc_start: 0.7706 (mmtp) cc_final: 0.7440 (mtmt) REVERT: A 1095 TYR cc_start: 0.7152 (t80) cc_final: 0.6949 (t80) REVERT: A 1126 PHE cc_start: 0.7627 (t80) cc_final: 0.7358 (m-80) REVERT: B 399 THR cc_start: 0.9289 (t) cc_final: 0.8967 (m) REVERT: B 410 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7875 (mmmm) REVERT: B 412 HIS cc_start: 0.6831 (p90) cc_final: 0.6592 (p90) REVERT: B 642 GLN cc_start: 0.8006 (pp30) cc_final: 0.7698 (pp30) REVERT: B 656 LYS cc_start: 0.8729 (tttt) cc_final: 0.8277 (ttmt) REVERT: B 684 ARG cc_start: 0.7990 (pmm150) cc_final: 0.7541 (mtm-85) REVERT: B 713 GLU cc_start: 0.7577 (tt0) cc_final: 0.7302 (tt0) REVERT: B 1035 SER cc_start: 0.8127 (p) cc_final: 0.7787 (t) REVERT: B 1119 LEU cc_start: 0.7361 (tt) cc_final: 0.6972 (tp) REVERT: B 1200 PHE cc_start: 0.8409 (t80) cc_final: 0.8134 (t80) REVERT: B 1202 ASP cc_start: 0.7815 (t70) cc_final: 0.7576 (t0) REVERT: C 414 MET cc_start: 0.7602 (mpt) cc_final: 0.7342 (mtp) REVERT: C 668 ASP cc_start: 0.7648 (t70) cc_final: 0.7362 (t0) REVERT: C 695 LYS cc_start: 0.8606 (mptt) cc_final: 0.8371 (pttp) REVERT: C 788 SER cc_start: 0.8751 (m) cc_final: 0.8469 (t) REVERT: C 813 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6730 (tp30) REVERT: C 1095 TYR cc_start: 0.7250 (t80) cc_final: 0.7044 (t80) REVERT: C 1114 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8659 (mm) REVERT: C 1173 TYR cc_start: 0.7832 (p90) cc_final: 0.7567 (p90) REVERT: D 410 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7771 (mmmm) REVERT: D 467 LEU cc_start: 0.8577 (mt) cc_final: 0.8367 (mt) REVERT: D 642 GLN cc_start: 0.7949 (pp30) cc_final: 0.7584 (pp30) REVERT: D 656 LYS cc_start: 0.8528 (tttt) cc_final: 0.8185 (ttmt) REVERT: D 684 ARG cc_start: 0.7915 (pmm150) cc_final: 0.7549 (mtm-85) REVERT: D 713 GLU cc_start: 0.7503 (tt0) cc_final: 0.7270 (tt0) REVERT: D 813 GLU cc_start: 0.7558 (pp20) cc_final: 0.7263 (tm-30) REVERT: D 1035 SER cc_start: 0.8152 (p) cc_final: 0.7792 (t) REVERT: D 1108 ILE cc_start: 0.8873 (mt) cc_final: 0.8616 (pt) REVERT: D 1115 PHE cc_start: 0.7943 (t80) cc_final: 0.7708 (t80) REVERT: D 1202 ASP cc_start: 0.7265 (t70) cc_final: 0.6778 (t0) outliers start: 8 outliers final: 0 residues processed: 560 average time/residue: 0.3247 time to fit residues: 269.7985 Evaluate side-chains 306 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1114 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 714 GLN A 756 GLN A1206 GLN B 791 ASN B1071 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C 756 GLN C1131 HIS C1206 GLN D 791 ASN D1071 ASN ** D1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111921 restraints weight = 30436.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113123 restraints weight = 21992.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113739 restraints weight = 16052.959| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19878 Z= 0.133 Angle : 0.592 9.387 26866 Z= 0.314 Chirality : 0.041 0.213 2998 Planarity : 0.004 0.043 3312 Dihedral : 8.680 103.828 2790 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.49 % Allowed : 11.94 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.24 (0.15), residues: 2460 helix: -0.04 (0.12), residues: 1330 sheet: -1.27 (0.39), residues: 142 loop : -1.79 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 766 HIS 0.017 0.002 HIS A1059 PHE 0.021 0.001 PHE D1200 TYR 0.022 0.001 TYR C 523 ARG 0.005 0.001 ARG D1036 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 1078) hydrogen bonds : angle 4.45345 ( 3138) SS BOND : bond 0.00272 ( 12) SS BOND : angle 1.34355 ( 24) covalent geometry : bond 0.00293 (19866) covalent geometry : angle 0.59094 (26842) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 399 time to evaluate : 2.034 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7632 (mpt) cc_final: 0.7368 (mtp) REVERT: A 1025 ILE cc_start: 0.8439 (mm) cc_final: 0.8209 (mm) REVERT: A 1126 PHE cc_start: 0.7528 (t80) cc_final: 0.7303 (m-80) REVERT: B 563 GLN cc_start: 0.5470 (mt0) cc_final: 0.4721 (tm-30) REVERT: B 642 GLN cc_start: 0.8188 (pp30) cc_final: 0.7842 (pp30) REVERT: B 656 LYS cc_start: 0.8468 (tttt) cc_final: 0.8201 (tmtt) REVERT: B 1009 MET cc_start: 0.8019 (tpp) cc_final: 0.7624 (tmm) REVERT: B 1032 TRP cc_start: 0.8423 (m100) cc_final: 0.8086 (m-10) REVERT: B 1035 SER cc_start: 0.8278 (p) cc_final: 0.7902 (t) REVERT: B 1199 MET cc_start: 0.8031 (mmm) cc_final: 0.7797 (mmt) REVERT: B 1200 PHE cc_start: 0.8334 (t80) cc_final: 0.8063 (t80) REVERT: C 414 MET cc_start: 0.7679 (mpt) cc_final: 0.7478 (mtp) REVERT: C 642 GLN cc_start: 0.8319 (pp30) cc_final: 0.8014 (pp30) REVERT: C 742 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7428 (pp) REVERT: C 813 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6667 (tp30) REVERT: C 1095 TYR cc_start: 0.7230 (t80) cc_final: 0.6686 (t80) REVERT: C 1150 ILE cc_start: 0.9004 (tp) cc_final: 0.8794 (tp) REVERT: D 684 ARG cc_start: 0.7737 (pmm150) cc_final: 0.7441 (mtm-85) REVERT: D 1035 SER cc_start: 0.8221 (p) cc_final: 0.7839 (t) REVERT: D 1202 ASP cc_start: 0.7058 (t70) cc_final: 0.6773 (t0) outliers start: 52 outliers final: 18 residues processed: 437 average time/residue: 0.2799 time to fit residues: 191.1681 Evaluate side-chains 324 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 305 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1191 MET Chi-restraints excluded: chain D residue 1172 SER Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 8 optimal weight: 0.0020 chunk 168 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107161 restraints weight = 30475.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108183 restraints weight = 16523.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108338 restraints weight = 13766.403| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19878 Z= 0.186 Angle : 0.599 8.420 26866 Z= 0.316 Chirality : 0.043 0.201 2998 Planarity : 0.004 0.038 3312 Dihedral : 8.240 96.588 2790 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.69 % Allowed : 14.19 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2460 helix: 1.25 (0.14), residues: 1330 sheet: -1.10 (0.41), residues: 142 loop : -1.66 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1063 HIS 0.015 0.002 HIS A1059 PHE 0.014 0.002 PHE D1072 TYR 0.023 0.001 TYR C 523 ARG 0.005 0.001 ARG D1036 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 1078) hydrogen bonds : angle 4.23842 ( 3138) SS BOND : bond 0.00472 ( 12) SS BOND : angle 0.99526 ( 24) covalent geometry : bond 0.00440 (19866) covalent geometry : angle 0.59827 (26842) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 317 time to evaluate : 1.955 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7770 (mpt) cc_final: 0.7516 (mtp) REVERT: A 642 GLN cc_start: 0.8472 (pp30) cc_final: 0.8129 (pp30) REVERT: A 817 LYS cc_start: 0.7496 (mmtp) cc_final: 0.7255 (mttt) REVERT: A 1025 ILE cc_start: 0.8459 (mm) cc_final: 0.8249 (mm) REVERT: A 1121 ILE cc_start: 0.7920 (tp) cc_final: 0.7700 (tt) REVERT: A 1126 PHE cc_start: 0.7484 (t80) cc_final: 0.7223 (m-80) REVERT: B 563 GLN cc_start: 0.5485 (mt0) cc_final: 0.4736 (tm-30) REVERT: B 642 GLN cc_start: 0.8238 (pp30) cc_final: 0.7897 (pp30) REVERT: B 647 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7374 (m-10) REVERT: B 656 LYS cc_start: 0.8514 (tttt) cc_final: 0.8273 (tmtt) REVERT: B 1005 ARG cc_start: 0.6588 (tmm-80) cc_final: 0.5994 (mtm110) REVERT: B 1009 MET cc_start: 0.8065 (tpp) cc_final: 0.7683 (tmm) REVERT: B 1032 TRP cc_start: 0.8456 (m100) cc_final: 0.8107 (m-10) REVERT: B 1035 SER cc_start: 0.8264 (p) cc_final: 0.7882 (t) REVERT: B 1113 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8561 (mt) REVERT: B 1199 MET cc_start: 0.8085 (mmm) cc_final: 0.7876 (mmt) REVERT: C 414 MET cc_start: 0.7778 (mpt) cc_final: 0.7555 (mtp) REVERT: C 642 GLN cc_start: 0.8432 (pp30) cc_final: 0.8113 (pp30) REVERT: C 742 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7523 (pp) REVERT: C 813 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6682 (tp30) REVERT: C 1095 TYR cc_start: 0.7305 (t80) cc_final: 0.6738 (t80) REVERT: C 1198 HIS cc_start: 0.8094 (m-70) cc_final: 0.7833 (m-70) REVERT: D 467 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8516 (mm) REVERT: D 486 GLU cc_start: 0.7577 (tp30) cc_final: 0.7235 (tp30) REVERT: D 647 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.7306 (m-10) REVERT: D 684 ARG cc_start: 0.7849 (pmm150) cc_final: 0.7554 (mtm-85) REVERT: D 1035 SER cc_start: 0.8154 (p) cc_final: 0.7732 (t) REVERT: D 1202 ASP cc_start: 0.7184 (t70) cc_final: 0.6789 (t0) outliers start: 77 outliers final: 43 residues processed: 370 average time/residue: 0.2654 time to fit residues: 158.3117 Evaluate side-chains 329 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 281 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Chi-restraints excluded: chain D residue 1192 VAL Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.104795 restraints weight = 30676.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106768 restraints weight = 18710.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107283 restraints weight = 14039.179| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 19878 Z= 0.236 Angle : 0.627 8.435 26866 Z= 0.331 Chirality : 0.044 0.213 2998 Planarity : 0.004 0.038 3312 Dihedral : 8.145 93.776 2790 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.93 % Allowed : 15.15 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2460 helix: 1.43 (0.14), residues: 1330 sheet: -1.07 (0.43), residues: 142 loop : -1.69 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1063 HIS 0.012 0.002 HIS A1059 PHE 0.017 0.002 PHE B1200 TYR 0.025 0.002 TYR C1155 ARG 0.004 0.001 ARG D1036 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 1078) hydrogen bonds : angle 4.32644 ( 3138) SS BOND : bond 0.00324 ( 12) SS BOND : angle 0.93586 ( 24) covalent geometry : bond 0.00564 (19866) covalent geometry : angle 0.62658 (26842) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 306 time to evaluate : 2.140 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7853 (mpt) cc_final: 0.7573 (mtp) REVERT: A 1126 PHE cc_start: 0.7424 (t80) cc_final: 0.7164 (m-80) REVERT: A 1204 HIS cc_start: 0.7266 (t-90) cc_final: 0.6975 (t-90) REVERT: B 642 GLN cc_start: 0.8245 (pp30) cc_final: 0.7952 (pp30) REVERT: B 647 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.7396 (m-10) REVERT: B 656 LYS cc_start: 0.8566 (tttt) cc_final: 0.8335 (tmtt) REVERT: B 1005 ARG cc_start: 0.6498 (tmm-80) cc_final: 0.5958 (mtm110) REVERT: B 1009 MET cc_start: 0.7969 (tpp) cc_final: 0.7602 (tmm) REVERT: B 1032 TRP cc_start: 0.8472 (m100) cc_final: 0.8139 (m-10) REVERT: B 1035 SER cc_start: 0.8185 (p) cc_final: 0.7812 (t) REVERT: C 742 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7642 (pp) REVERT: C 813 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6709 (tp30) REVERT: C 1095 TYR cc_start: 0.7407 (t80) cc_final: 0.6810 (t80) REVERT: C 1198 HIS cc_start: 0.8226 (m-70) cc_final: 0.8023 (m-70) REVERT: D 467 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8517 (mm) REVERT: D 486 GLU cc_start: 0.7795 (tp30) cc_final: 0.7436 (tp30) REVERT: D 647 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.7400 (m-10) REVERT: D 684 ARG cc_start: 0.7846 (pmm150) cc_final: 0.7521 (mtm-85) REVERT: D 705 GLU cc_start: 0.7887 (mp0) cc_final: 0.7649 (mp0) REVERT: D 1032 TRP cc_start: 0.8444 (m100) cc_final: 0.8090 (m-10) REVERT: D 1035 SER cc_start: 0.8042 (p) cc_final: 0.7688 (t) REVERT: D 1069 GLU cc_start: 0.6438 (tp30) cc_final: 0.6170 (tm-30) REVERT: D 1077 LYS cc_start: 0.7946 (pttt) cc_final: 0.6661 (ptpp) REVERT: D 1202 ASP cc_start: 0.7167 (t70) cc_final: 0.6876 (t0) outliers start: 82 outliers final: 49 residues processed: 359 average time/residue: 0.2613 time to fit residues: 152.1077 Evaluate side-chains 333 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Chi-restraints excluded: chain D residue 1192 VAL Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 145 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 chunk 197 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 412 HIS B 563 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1008 GLN D1198 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109607 restraints weight = 30519.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110721 restraints weight = 16723.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111077 restraints weight = 13554.128| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19878 Z= 0.115 Angle : 0.538 7.923 26866 Z= 0.282 Chirality : 0.040 0.180 2998 Planarity : 0.003 0.035 3312 Dihedral : 7.482 88.041 2790 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.83 % Allowed : 16.44 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2460 helix: 1.97 (0.14), residues: 1342 sheet: -1.09 (0.43), residues: 142 loop : -1.64 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 766 HIS 0.010 0.001 HIS A1059 PHE 0.013 0.001 PHE C 495 TYR 0.024 0.001 TYR A1155 ARG 0.004 0.000 ARG D 675 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 1078) hydrogen bonds : angle 3.94352 ( 3138) SS BOND : bond 0.00144 ( 12) SS BOND : angle 1.53125 ( 24) covalent geometry : bond 0.00259 (19866) covalent geometry : angle 0.53585 (26842) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 331 time to evaluate : 2.306 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7887 (mpt) cc_final: 0.7597 (mtp) REVERT: A 642 GLN cc_start: 0.8425 (pp30) cc_final: 0.8178 (pp30) REVERT: A 1126 PHE cc_start: 0.7396 (t80) cc_final: 0.7172 (m-80) REVERT: B 486 GLU cc_start: 0.7840 (tp30) cc_final: 0.7514 (tp30) REVERT: B 563 GLN cc_start: 0.5768 (mt0) cc_final: 0.4810 (tm-30) REVERT: B 589 CYS cc_start: 0.6750 (t) cc_final: 0.6512 (t) REVERT: B 613 ILE cc_start: 0.9271 (mm) cc_final: 0.9032 (mm) REVERT: B 1005 ARG cc_start: 0.6428 (tmm-80) cc_final: 0.5558 (mtm110) REVERT: B 1032 TRP cc_start: 0.8456 (m100) cc_final: 0.8107 (m-10) REVERT: B 1035 SER cc_start: 0.8221 (p) cc_final: 0.7827 (t) REVERT: B 1069 GLU cc_start: 0.6413 (tp30) cc_final: 0.6093 (tm-30) REVERT: B 1077 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.6523 (ptpp) REVERT: C 642 GLN cc_start: 0.8464 (pp30) cc_final: 0.8192 (pp30) REVERT: C 1095 TYR cc_start: 0.7286 (t80) cc_final: 0.6782 (t80) REVERT: D 467 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8502 (mm) REVERT: D 486 GLU cc_start: 0.7684 (tp30) cc_final: 0.7283 (tp30) REVERT: D 684 ARG cc_start: 0.7853 (pmm150) cc_final: 0.7558 (mtm-85) REVERT: D 705 GLU cc_start: 0.7874 (mp0) cc_final: 0.7657 (mp0) REVERT: D 1032 TRP cc_start: 0.8450 (m100) cc_final: 0.8099 (m-10) REVERT: D 1035 SER cc_start: 0.8098 (p) cc_final: 0.7719 (t) REVERT: D 1077 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.6575 (ptpp) REVERT: D 1115 PHE cc_start: 0.7984 (t80) cc_final: 0.7720 (t80) REVERT: D 1202 ASP cc_start: 0.7297 (t70) cc_final: 0.6978 (t0) outliers start: 59 outliers final: 32 residues processed: 367 average time/residue: 0.2675 time to fit residues: 158.7576 Evaluate side-chains 322 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1077 LYS Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105891 restraints weight = 30681.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107147 restraints weight = 16962.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107370 restraints weight = 13700.458| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19878 Z= 0.190 Angle : 0.581 7.062 26866 Z= 0.306 Chirality : 0.043 0.200 2998 Planarity : 0.003 0.035 3312 Dihedral : 7.364 88.728 2790 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.50 % Allowed : 17.35 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2460 helix: 1.84 (0.14), residues: 1344 sheet: -1.17 (0.43), residues: 142 loop : -1.65 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1063 HIS 0.008 0.001 HIS A1059 PHE 0.014 0.002 PHE D 438 TYR 0.025 0.001 TYR A1155 ARG 0.004 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1078) hydrogen bonds : angle 4.10531 ( 3138) SS BOND : bond 0.00188 ( 12) SS BOND : angle 1.45379 ( 24) covalent geometry : bond 0.00452 (19866) covalent geometry : angle 0.58007 (26842) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 288 time to evaluate : 2.327 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7923 (mpt) cc_final: 0.7627 (mtp) REVERT: A 1126 PHE cc_start: 0.7374 (t80) cc_final: 0.7134 (m-80) REVERT: B 563 GLN cc_start: 0.5744 (OUTLIER) cc_final: 0.4643 (tm-30) REVERT: B 656 LYS cc_start: 0.8287 (tmtt) cc_final: 0.7991 (tmtt) REVERT: B 1005 ARG cc_start: 0.5692 (tmm-80) cc_final: 0.5372 (mtm110) REVERT: B 1009 MET cc_start: 0.8092 (tpp) cc_final: 0.7776 (tpp) REVERT: B 1032 TRP cc_start: 0.8497 (m100) cc_final: 0.8112 (m-10) REVERT: B 1035 SER cc_start: 0.8207 (p) cc_final: 0.7824 (t) REVERT: B 1199 MET cc_start: 0.8286 (mmt) cc_final: 0.7988 (mmp) REVERT: C 427 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7328 (t0) REVERT: C 1063 TRP cc_start: 0.7933 (m-90) cc_final: 0.7576 (m-90) REVERT: C 1095 TYR cc_start: 0.7409 (t80) cc_final: 0.6878 (t80) REVERT: C 1150 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8827 (tp) REVERT: D 467 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8537 (mm) REVERT: D 563 GLN cc_start: 0.5567 (mt0) cc_final: 0.4780 (tm-30) REVERT: D 684 ARG cc_start: 0.7890 (pmm150) cc_final: 0.7582 (mtm-85) REVERT: D 705 GLU cc_start: 0.7903 (mp0) cc_final: 0.7667 (mp0) REVERT: D 1032 TRP cc_start: 0.8470 (m100) cc_final: 0.8096 (m-10) REVERT: D 1035 SER cc_start: 0.8056 (p) cc_final: 0.7700 (t) REVERT: D 1044 VAL cc_start: 0.5349 (OUTLIER) cc_final: 0.5105 (t) REVERT: D 1069 GLU cc_start: 0.6491 (tp30) cc_final: 0.6167 (tm-30) REVERT: D 1077 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.6552 (ptpp) REVERT: D 1202 ASP cc_start: 0.7345 (t70) cc_final: 0.7021 (t0) outliers start: 73 outliers final: 48 residues processed: 331 average time/residue: 0.2526 time to fit residues: 136.9394 Evaluate side-chains 331 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 277 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1150 ILE Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 208 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104297 restraints weight = 30741.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106807 restraints weight = 21285.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107552 restraints weight = 14390.503| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19878 Z= 0.240 Angle : 0.625 7.443 26866 Z= 0.330 Chirality : 0.045 0.247 2998 Planarity : 0.004 0.036 3312 Dihedral : 7.271 88.267 2790 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.79 % Allowed : 18.07 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2460 helix: 1.67 (0.14), residues: 1334 sheet: -1.30 (0.43), residues: 142 loop : -1.69 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1063 HIS 0.008 0.001 HIS B 412 PHE 0.017 0.002 PHE A1115 TYR 0.027 0.002 TYR B 647 ARG 0.003 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 1078) hydrogen bonds : angle 4.26347 ( 3138) SS BOND : bond 0.00290 ( 12) SS BOND : angle 1.47331 ( 24) covalent geometry : bond 0.00572 (19866) covalent geometry : angle 0.62400 (26842) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 284 time to evaluate : 2.015 Fit side-chains REVERT: A 407 MET cc_start: 0.8306 (mtm) cc_final: 0.7972 (mtm) REVERT: A 414 MET cc_start: 0.7857 (mpt) cc_final: 0.7564 (mtp) REVERT: A 450 TYR cc_start: 0.8276 (m-80) cc_final: 0.7796 (m-80) REVERT: A 642 GLN cc_start: 0.8345 (pp30) cc_final: 0.8088 (pp30) REVERT: A 1126 PHE cc_start: 0.7323 (t80) cc_final: 0.7103 (m-80) REVERT: B 563 GLN cc_start: 0.5805 (OUTLIER) cc_final: 0.4740 (tm-30) REVERT: B 1032 TRP cc_start: 0.8498 (m100) cc_final: 0.8130 (m-10) REVERT: B 1035 SER cc_start: 0.8159 (p) cc_final: 0.7780 (t) REVERT: C 642 GLN cc_start: 0.8370 (pp30) cc_final: 0.8104 (pp30) REVERT: C 1095 TYR cc_start: 0.7470 (t80) cc_final: 0.6917 (t80) REVERT: C 1150 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8884 (tp) REVERT: D 407 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8367 (mtp) REVERT: D 467 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8527 (mm) REVERT: D 684 ARG cc_start: 0.7860 (pmm150) cc_final: 0.7550 (mtm-85) REVERT: D 705 GLU cc_start: 0.7898 (mp0) cc_final: 0.7649 (mp0) REVERT: D 1032 TRP cc_start: 0.8495 (m100) cc_final: 0.8129 (m-10) REVERT: D 1035 SER cc_start: 0.8079 (p) cc_final: 0.7757 (t) REVERT: D 1044 VAL cc_start: 0.5300 (OUTLIER) cc_final: 0.5055 (t) REVERT: D 1069 GLU cc_start: 0.6371 (tp30) cc_final: 0.6097 (tm-30) REVERT: D 1077 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.6649 (ptpt) REVERT: D 1202 ASP cc_start: 0.7342 (t70) cc_final: 0.7012 (t0) outliers start: 79 outliers final: 60 residues processed: 337 average time/residue: 0.2485 time to fit residues: 137.4824 Evaluate side-chains 332 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1150 ILE Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 784 THR Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 813 GLU Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 229 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108688 restraints weight = 30515.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109873 restraints weight = 17176.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110330 restraints weight = 14072.206| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19878 Z= 0.118 Angle : 0.537 7.043 26866 Z= 0.281 Chirality : 0.041 0.212 2998 Planarity : 0.003 0.034 3312 Dihedral : 6.484 82.930 2790 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.59 % Allowed : 19.85 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2460 helix: 2.15 (0.14), residues: 1336 sheet: -1.31 (0.43), residues: 142 loop : -1.60 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 766 HIS 0.009 0.001 HIS A1059 PHE 0.017 0.001 PHE D 438 TYR 0.023 0.001 TYR A1155 ARG 0.004 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 1078) hydrogen bonds : angle 3.90953 ( 3138) SS BOND : bond 0.00139 ( 12) SS BOND : angle 0.91165 ( 24) covalent geometry : bond 0.00268 (19866) covalent geometry : angle 0.53683 (26842) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 323 time to evaluate : 2.207 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8314 (mtm) cc_final: 0.8103 (mtm) REVERT: A 414 MET cc_start: 0.7987 (mpt) cc_final: 0.7681 (mtp) REVERT: A 450 TYR cc_start: 0.8185 (m-80) cc_final: 0.7852 (m-80) REVERT: A 642 GLN cc_start: 0.8334 (pp30) cc_final: 0.8019 (pp30) REVERT: A 1023 MET cc_start: 0.9001 (tpt) cc_final: 0.8690 (tpt) REVERT: A 1126 PHE cc_start: 0.7287 (t80) cc_final: 0.7048 (m-80) REVERT: B 467 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8483 (mm) REVERT: B 486 GLU cc_start: 0.7804 (tp30) cc_final: 0.7440 (tp30) REVERT: B 563 GLN cc_start: 0.5759 (OUTLIER) cc_final: 0.4772 (tm-30) REVERT: B 1032 TRP cc_start: 0.8498 (m100) cc_final: 0.8156 (m-10) REVERT: B 1035 SER cc_start: 0.8131 (p) cc_final: 0.7741 (t) REVERT: C 642 GLN cc_start: 0.8352 (pp30) cc_final: 0.8044 (pp30) REVERT: C 1063 TRP cc_start: 0.7901 (m-90) cc_final: 0.7607 (m-90) REVERT: C 1095 TYR cc_start: 0.7427 (t80) cc_final: 0.6887 (t80) REVERT: D 467 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8500 (mm) REVERT: D 563 GLN cc_start: 0.5784 (mt0) cc_final: 0.4826 (tm-30) REVERT: D 656 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8028 (tmtt) REVERT: D 684 ARG cc_start: 0.7862 (pmm150) cc_final: 0.7566 (mtm-85) REVERT: D 1032 TRP cc_start: 0.8487 (m100) cc_final: 0.8142 (m-10) REVERT: D 1035 SER cc_start: 0.7977 (p) cc_final: 0.7683 (t) REVERT: D 1069 GLU cc_start: 0.6430 (tp30) cc_final: 0.6030 (tm-30) REVERT: D 1077 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.6427 (ptpp) REVERT: D 1202 ASP cc_start: 0.7402 (t70) cc_final: 0.7045 (t0) outliers start: 54 outliers final: 40 residues processed: 358 average time/residue: 0.2551 time to fit residues: 148.6739 Evaluate side-chains 334 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 162 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 245 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109306 restraints weight = 30410.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111696 restraints weight = 19803.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112496 restraints weight = 13680.510| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19878 Z= 0.122 Angle : 0.544 8.082 26866 Z= 0.285 Chirality : 0.041 0.194 2998 Planarity : 0.003 0.033 3312 Dihedral : 6.045 79.435 2790 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.54 % Allowed : 20.52 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2460 helix: 2.25 (0.14), residues: 1336 sheet: -1.27 (0.43), residues: 142 loop : -1.56 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 766 HIS 0.010 0.001 HIS B 412 PHE 0.016 0.001 PHE D 438 TYR 0.022 0.001 TYR C1155 ARG 0.004 0.000 ARG B1005 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 1078) hydrogen bonds : angle 3.85441 ( 3138) SS BOND : bond 0.00186 ( 12) SS BOND : angle 0.86994 ( 24) covalent geometry : bond 0.00280 (19866) covalent geometry : angle 0.54337 (26842) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 1.968 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8340 (mtm) cc_final: 0.8134 (mtm) REVERT: A 414 MET cc_start: 0.7919 (mpt) cc_final: 0.7642 (mtp) REVERT: A 450 TYR cc_start: 0.8213 (m-80) cc_final: 0.7837 (m-80) REVERT: A 642 GLN cc_start: 0.8341 (pp30) cc_final: 0.8079 (pp30) REVERT: A 1023 MET cc_start: 0.8969 (tpt) cc_final: 0.8717 (tpt) REVERT: B 467 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8508 (mm) REVERT: B 486 GLU cc_start: 0.7747 (tp30) cc_final: 0.7387 (tp30) REVERT: B 563 GLN cc_start: 0.5789 (OUTLIER) cc_final: 0.4785 (tm-30) REVERT: B 1005 ARG cc_start: 0.5821 (tmm-80) cc_final: 0.5363 (mtm110) REVERT: B 1032 TRP cc_start: 0.8453 (m100) cc_final: 0.8108 (m-10) REVERT: B 1035 SER cc_start: 0.8251 (p) cc_final: 0.7849 (t) REVERT: B 1199 MET cc_start: 0.8462 (mmt) cc_final: 0.8260 (mmp) REVERT: C 642 GLN cc_start: 0.8356 (pp30) cc_final: 0.8086 (pp30) REVERT: C 1063 TRP cc_start: 0.7936 (m-90) cc_final: 0.7671 (m-90) REVERT: C 1095 TYR cc_start: 0.7449 (t80) cc_final: 0.6980 (t80) REVERT: D 407 MET cc_start: 0.8241 (mtm) cc_final: 0.8033 (mtm) REVERT: D 467 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8484 (mm) REVERT: D 486 GLU cc_start: 0.7695 (tp30) cc_final: 0.7314 (tp30) REVERT: D 563 GLN cc_start: 0.5860 (mt0) cc_final: 0.4858 (tm-30) REVERT: D 656 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8075 (tmtt) REVERT: D 684 ARG cc_start: 0.7867 (pmm150) cc_final: 0.7529 (mtm-85) REVERT: D 1032 TRP cc_start: 0.8417 (m100) cc_final: 0.8093 (m-10) REVERT: D 1035 SER cc_start: 0.8145 (p) cc_final: 0.7840 (t) REVERT: D 1069 GLU cc_start: 0.6371 (tp30) cc_final: 0.6058 (tm-30) REVERT: D 1077 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.6458 (ptpp) REVERT: D 1202 ASP cc_start: 0.7366 (t70) cc_final: 0.7056 (t0) outliers start: 53 outliers final: 47 residues processed: 333 average time/residue: 0.2623 time to fit residues: 140.5502 Evaluate side-chains 341 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 813 GLU Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 37 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 193 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS B1131 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111004 restraints weight = 30300.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113936 restraints weight = 19144.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114506 restraints weight = 13322.893| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19878 Z= 0.112 Angle : 0.541 8.321 26866 Z= 0.282 Chirality : 0.040 0.193 2998 Planarity : 0.003 0.031 3312 Dihedral : 5.653 71.640 2790 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.35 % Allowed : 20.81 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2460 helix: 2.34 (0.14), residues: 1338 sheet: -1.26 (0.43), residues: 142 loop : -1.53 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 460 HIS 0.011 0.001 HIS B 412 PHE 0.021 0.001 PHE B 438 TYR 0.022 0.001 TYR A1155 ARG 0.004 0.000 ARG B1005 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 1078) hydrogen bonds : angle 3.78810 ( 3138) SS BOND : bond 0.00226 ( 12) SS BOND : angle 0.87116 ( 24) covalent geometry : bond 0.00256 (19866) covalent geometry : angle 0.54070 (26842) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 310 time to evaluate : 2.144 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8310 (mtm) cc_final: 0.8098 (mtm) REVERT: A 414 MET cc_start: 0.7916 (mpt) cc_final: 0.7650 (mtp) REVERT: A 450 TYR cc_start: 0.8223 (m-80) cc_final: 0.7794 (m-80) REVERT: A 642 GLN cc_start: 0.8338 (pp30) cc_final: 0.8105 (pp30) REVERT: A 1023 MET cc_start: 0.8900 (tpt) cc_final: 0.8696 (tpt) REVERT: B 467 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8534 (mm) REVERT: B 486 GLU cc_start: 0.7707 (tp30) cc_final: 0.7344 (tp30) REVERT: B 563 GLN cc_start: 0.5731 (OUTLIER) cc_final: 0.4771 (tm-30) REVERT: B 1005 ARG cc_start: 0.5788 (tmm-80) cc_final: 0.5319 (mtm110) REVERT: B 1032 TRP cc_start: 0.8469 (m100) cc_final: 0.8124 (m-10) REVERT: B 1035 SER cc_start: 0.8208 (p) cc_final: 0.7794 (t) REVERT: C 519 ASP cc_start: 0.7565 (m-30) cc_final: 0.7244 (m-30) REVERT: C 642 GLN cc_start: 0.8357 (pp30) cc_final: 0.8144 (pp30) REVERT: C 742 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7389 (pp) REVERT: C 1095 TYR cc_start: 0.7454 (t80) cc_final: 0.6938 (t80) REVERT: D 467 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8509 (mm) REVERT: D 486 GLU cc_start: 0.7694 (tp30) cc_final: 0.7304 (tp30) REVERT: D 563 GLN cc_start: 0.5975 (mt0) cc_final: 0.4744 (tm-30) REVERT: D 656 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8056 (tmtt) REVERT: D 684 ARG cc_start: 0.7858 (pmm150) cc_final: 0.7522 (mtm-85) REVERT: D 1032 TRP cc_start: 0.8417 (m100) cc_final: 0.8104 (m-10) REVERT: D 1035 SER cc_start: 0.8181 (p) cc_final: 0.7862 (t) REVERT: D 1069 GLU cc_start: 0.6261 (tp30) cc_final: 0.5990 (tm-30) REVERT: D 1077 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6476 (ptpp) REVERT: D 1202 ASP cc_start: 0.7378 (t70) cc_final: 0.7042 (t0) outliers start: 49 outliers final: 40 residues processed: 338 average time/residue: 0.2857 time to fit residues: 157.8564 Evaluate side-chains 335 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 290 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1030 ASP Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 181 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS B1131 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107510 restraints weight = 30750.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110218 restraints weight = 21280.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110843 restraints weight = 14455.446| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19878 Z= 0.169 Angle : 0.580 8.515 26866 Z= 0.304 Chirality : 0.042 0.193 2998 Planarity : 0.003 0.032 3312 Dihedral : 5.727 69.625 2790 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.78 % Allowed : 20.66 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2460 helix: 2.16 (0.14), residues: 1336 sheet: -1.27 (0.43), residues: 142 loop : -1.56 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1063 HIS 0.011 0.001 HIS B 412 PHE 0.017 0.002 PHE B1126 TYR 0.023 0.001 TYR C 523 ARG 0.004 0.000 ARG B1005 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 1078) hydrogen bonds : angle 3.93432 ( 3138) SS BOND : bond 0.00234 ( 12) SS BOND : angle 0.99110 ( 24) covalent geometry : bond 0.00404 (19866) covalent geometry : angle 0.57939 (26842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5845.35 seconds wall clock time: 102 minutes 25.91 seconds (6145.91 seconds total)