Starting phenix.real_space_refine on Sat Jul 4 08:08:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnl_26013/07_2026/7tnl_26013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnl_26013/07_2026/7tnl_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tnl_26013/07_2026/7tnl_26013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnl_26013/07_2026/7tnl_26013.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tnl_26013/07_2026/7tnl_26013.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnl_26013/07_2026/7tnl_26013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tnl_26013/07_2026/7tnl_26013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnl_26013/07_2026/7tnl_26013.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.43, per 1000 atoms: 0.18 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: 1.38 Conformation dependent library (CDL) restraints added in 558.3 milliseconds 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: 0.52 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: 2.87 Time building geometry restraints manager: 1.84 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 - 19.36: 11166 19.36 - 38.73: 464 38.73 - 58.09: 56 58.09 - 77.45: 10 77.45 - 96.81: 4 Dihedral angle restraints: 11700 sinusoidal: 4570 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 11697 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: 0.02 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.030 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 10.968 96.813 7116 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.012 0.001 ARG A 599 TYR 0.028 0.003 TYR D 702 PHE 0.038 0.003 PHE C 623 TRP 0.024 0.005 TRP A 671 HIS 0.007 0.003 HIS A1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00921 / 0.38 (19866) covalent geometry : angle 1.02879 / 0.56 (26842) SS BOND : bond 0.01176 / 0.81 ( 12) SS BOND : angle 1.90627 / 1.30 ( 24) hydrogen bonds : bond 0.27055 / 17.68 ( 1078) hydrogen bonds : angle 8.99511 / 6.31 ( 3138) *********************** 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 : 0.750 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 490 ASP cc_start: 0.8589 (m-30) cc_final: 0.7996 (p0) 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: 0.7441 (mtmt) REVERT: A 1095 TYR cc_start: 0.7152 (t80) cc_final: 0.6948 (t80) REVERT: A 1126 PHE cc_start: 0.7627 (t80) cc_final: 0.7359 (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: 0.7876 (mmmm) REVERT: B 412 HIS cc_start: 0.6831 (p90) cc_final: 0.6593 (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: 0.7788 (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: 0.8135 (t80) REVERT: B 1202 ASP cc_start: 0.7816 (t70) cc_final: 0.7566 (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: 0.8470 (t) REVERT: C 813 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6732 (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: 0.7566 (p90) REVERT: D 410 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7773 (mmmm) REVERT: D 467 LEU cc_start: 0.8577 (mt) cc_final: 0.8368 (mt) REVERT: D 642 GLN cc_start: 0.7949 (pp30) cc_final: 0.7583 (pp30) REVERT: D 645 ILE cc_start: 0.7331 (mp) cc_final: 0.7130 (mt) REVERT: D 656 LYS cc_start: 0.8528 (tttt) cc_final: 0.8184 (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: 0.7791 (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: 0.7711 (t80) REVERT: D 1202 ASP cc_start: 0.7265 (t70) cc_final: 0.7054 (t0) outliers start: 8 outliers final: 0 residues processed: 560 average time/residue: 0.1352 time to fit residues: 114.0688 Evaluate side-chains 308 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3688 r_free = 0.3688 target = 0.139765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109963 restraints weight = 30377.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110867 restraints weight = 21262.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111442 restraints weight = 16068.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111908 restraints weight = 14227.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111984 restraints weight = 13523.178| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19878 Z= 0.158 Angle : 0.605 9.779 26866 Z= 0.322 Chirality : 0.042 0.215 2998 Planarity : 0.005 0.043 3312 Dihedral : 6.288 89.645 2694 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.73 % Allowed : 11.74 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.15), residues: 2460 helix: -0.08 (0.12), residues: 1330 sheet: -1.34 (0.38), residues: 152 loop : -1.78 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1036 TYR 0.023 0.001 TYR C 523 PHE 0.022 0.002 PHE D1200 TRP 0.013 0.002 TRP D 767 HIS 0.018 0.002 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (19866) covalent geometry : angle 0.60394 / 0.32 (26842) SS BOND : bond 0.00497 / 0.37 ( 12) SS BOND : angle 1.37004 / 0.94 ( 24) hydrogen bonds : bond 0.04663 / 3.04 ( 1078) hydrogen bonds : angle 4.48776 / 3.16 ( 3138) *********************** 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 439 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 382 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7630 (mpt) cc_final: 0.7358 (mtp) REVERT: A 742 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7291 (pp) REVERT: A 1025 ILE cc_start: 0.8434 (mm) cc_final: 0.8210 (mm) REVERT: A 1126 PHE cc_start: 0.7556 (t80) cc_final: 0.7316 (m-80) REVERT: B 563 GLN cc_start: 0.5506 (mt0) cc_final: 0.4743 (tm-30) REVERT: B 642 GLN cc_start: 0.8177 (pp30) cc_final: 0.7808 (pp30) REVERT: B 656 LYS cc_start: 0.8471 (tttt) cc_final: 0.8208 (tmtt) REVERT: B 1009 MET cc_start: 0.8014 (tpp) cc_final: 0.7635 (tmm) REVERT: B 1032 TRP cc_start: 0.8416 (m100) cc_final: 0.8077 (m-10) REVERT: B 1035 SER cc_start: 0.8283 (p) cc_final: 0.7911 (t) REVERT: B 1119 LEU cc_start: 0.7597 (tt) cc_final: 0.7099 (tp) REVERT: B 1199 MET cc_start: 0.7996 (mmm) cc_final: 0.7782 (mmt) REVERT: C 414 MET cc_start: 0.7688 (mpt) cc_final: 0.7483 (mtp) REVERT: C 642 GLN cc_start: 0.8354 (pp30) cc_final: 0.8062 (pp30) REVERT: C 742 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7465 (pp) REVERT: C 813 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6670 (tp30) REVERT: C 1095 TYR cc_start: 0.7187 (t80) cc_final: 0.6668 (t80) REVERT: C 1148 ASN cc_start: 0.8505 (t0) cc_final: 0.8276 (t0) REVERT: D 684 ARG cc_start: 0.7766 (pmm150) cc_final: 0.7442 (mtm-85) REVERT: D 1005 ARG cc_start: 0.6545 (tmm-80) cc_final: 0.6234 (ttm170) REVERT: D 1035 SER cc_start: 0.8176 (p) cc_final: 0.7805 (t) REVERT: D 1115 PHE cc_start: 0.8088 (t80) cc_final: 0.7886 (t80) REVERT: D 1202 ASP cc_start: 0.7110 (t70) cc_final: 0.6744 (t0) outliers start: 57 outliers final: 23 residues processed: 424 average time/residue: 0.1212 time to fit residues: 81.1652 Evaluate side-chains 319 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 294 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 742 LEU Chi-restraints excluded: chain A residue 1010 LEU 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 543 VAL 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 543 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 106 optimal weight: 9.9990 chunk 232 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 133 optimal weight: 0.1980 chunk 71 optimal weight: 0.0470 chunk 166 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 HIS C 756 GLN ** D1008 GLN ** 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 = 0.3708 r_free = 0.3708 target = 0.142044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112086 restraints weight = 30423.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113866 restraints weight = 18814.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114185 restraints weight = 13912.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114599 restraints weight = 13019.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114730 restraints weight = 11769.848| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19878 Z= 0.113 Angle : 0.528 8.221 26866 Z= 0.279 Chirality : 0.040 0.169 2998 Planarity : 0.003 0.036 3312 Dihedral : 5.773 85.678 2694 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.68 % Allowed : 15.05 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2460 helix: 1.43 (0.14), residues: 1332 sheet: -1.05 (0.40), residues: 142 loop : -1.62 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 628 TYR 0.020 0.001 TYR C 523 PHE 0.014 0.001 PHE B1141 TRP 0.014 0.001 TRP B1063 HIS 0.015 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (19866) covalent geometry : angle 0.52786 / 0.28 (26842) SS BOND : bond 0.00135 / 0.08 ( 12) SS BOND : angle 0.84867 / 0.57 ( 24) hydrogen bonds : bond 0.03807 / 2.49 ( 1078) hydrogen bonds : angle 4.00988 / 2.79 ( 3138) *********************** 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 387 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 331 time to evaluate : 0.645 Fit side-chains REVERT: A 431 GLU cc_start: 0.8227 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 519 ASP cc_start: 0.7649 (m-30) cc_final: 0.7286 (m-30) REVERT: A 642 GLN cc_start: 0.8475 (pp30) cc_final: 0.8136 (pp30) REVERT: A 1025 ILE cc_start: 0.8444 (mm) cc_final: 0.8243 (mm) REVERT: B 563 GLN cc_start: 0.5344 (mt0) cc_final: 0.4779 (tm-30) REVERT: B 613 ILE cc_start: 0.9196 (mm) cc_final: 0.8880 (mm) REVERT: B 642 GLN cc_start: 0.8189 (pp30) cc_final: 0.7878 (pp30) REVERT: B 656 LYS cc_start: 0.8470 (tttt) cc_final: 0.8163 (ttmt) REVERT: B 1005 ARG cc_start: 0.6335 (tmm-80) cc_final: 0.5861 (mtm110) REVERT: B 1032 TRP cc_start: 0.8449 (m100) cc_final: 0.8070 (m-10) REVERT: B 1035 SER cc_start: 0.8327 (p) cc_final: 0.7897 (t) REVERT: B 1056 VAL cc_start: 0.5043 (OUTLIER) cc_final: 0.4802 (p) REVERT: B 1113 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 414 MET cc_start: 0.7811 (mpt) cc_final: 0.7596 (mtp) REVERT: C 642 GLN cc_start: 0.8379 (pp30) cc_final: 0.8074 (pp30) REVERT: C 742 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7413 (pp) REVERT: C 813 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6624 (tp30) REVERT: C 819 ARG cc_start: 0.6124 (ppp80) cc_final: 0.5705 (ttm-80) REVERT: C 1095 TYR cc_start: 0.7116 (t80) cc_final: 0.6625 (t80) REVERT: C 1198 HIS cc_start: 0.8029 (m-70) cc_final: 0.7755 (m-70) REVERT: D 467 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8512 (mm) REVERT: D 684 ARG cc_start: 0.7744 (pmm150) cc_final: 0.7479 (mtm-85) REVERT: D 1025 ILE cc_start: 0.8618 (mm) cc_final: 0.8384 (tt) REVERT: D 1035 SER cc_start: 0.8251 (p) cc_final: 0.7551 (t) REVERT: D 1077 LYS cc_start: 0.8001 (tttt) cc_final: 0.6726 (ptpp) REVERT: D 1115 PHE cc_start: 0.8013 (t80) cc_final: 0.7799 (t80) REVERT: D 1202 ASP cc_start: 0.7188 (t70) cc_final: 0.6791 (t0) outliers start: 56 outliers final: 25 residues processed: 367 average time/residue: 0.1123 time to fit residues: 67.0489 Evaluate side-chains 317 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 288 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 666 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 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain B residue 1113 LEU 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 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 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 467 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1185 SER 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 165 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102897 restraints weight = 31054.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103966 restraints weight = 16702.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104027 restraints weight = 13988.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104225 restraints weight = 13870.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.104391 restraints weight = 12985.811| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 19878 Z= 0.318 Angle : 0.693 8.146 26866 Z= 0.367 Chirality : 0.047 0.218 2998 Planarity : 0.005 0.045 3312 Dihedral : 6.327 90.673 2694 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.65 % Allowed : 14.14 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2460 helix: 1.30 (0.14), residues: 1328 sheet: -1.04 (0.43), residues: 142 loop : -1.71 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1203 TYR 0.027 0.002 TYR C 523 PHE 0.020 0.003 PHE A1115 TRP 0.013 0.002 TRP A1063 HIS 0.012 0.002 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.32 (19866) covalent geometry : angle 0.69223 / 0.37 (26842) SS BOND : bond 0.00295 / 0.20 ( 12) SS BOND : angle 1.05290 / 0.74 ( 24) hydrogen bonds : bond 0.04893 / 3.18 ( 1078) hydrogen bonds : angle 4.50204 / 3.13 ( 3138) *********************** 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: 97 poor density : 291 time to evaluate : 0.679 Fit side-chains REVERT: A 1025 ILE cc_start: 0.8499 (mm) cc_final: 0.8272 (mm) REVERT: A 1204 HIS cc_start: 0.7367 (t-90) cc_final: 0.7063 (t-90) REVERT: B 642 GLN cc_start: 0.8258 (pp30) cc_final: 0.7940 (pp30) REVERT: B 647 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: B 656 LYS cc_start: 0.8611 (tttt) cc_final: 0.8351 (tmtt) REVERT: B 705 GLU cc_start: 0.7880 (mp0) cc_final: 0.7651 (mp0) REVERT: B 1005 ARG cc_start: 0.6519 (tmm-80) cc_final: 0.6133 (ttt180) REVERT: B 1032 TRP cc_start: 0.8510 (m100) cc_final: 0.8142 (m-10) REVERT: B 1035 SER cc_start: 0.8148 (p) cc_final: 0.7740 (t) REVERT: B 1125 GLU cc_start: 0.7717 (tp30) cc_final: 0.7455 (tm-30) REVERT: C 414 MET cc_start: 0.7822 (mpt) cc_final: 0.7592 (mtp) REVERT: C 742 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7653 (pp) REVERT: C 813 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6593 (tp30) REVERT: C 1095 TYR cc_start: 0.7383 (t80) cc_final: 0.6736 (t80) REVERT: C 1198 HIS cc_start: 0.8258 (m-70) cc_final: 0.8042 (m-70) REVERT: D 486 GLU cc_start: 0.7947 (tp30) cc_final: 0.7653 (tp30) REVERT: D 647 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7336 (m-10) REVERT: D 684 ARG cc_start: 0.7889 (pmm150) cc_final: 0.7559 (mtm-85) REVERT: D 705 GLU cc_start: 0.7920 (mp0) cc_final: 0.7686 (mp0) REVERT: D 1032 TRP cc_start: 0.8472 (m100) cc_final: 0.8103 (m-10) REVERT: D 1035 SER cc_start: 0.7980 (p) cc_final: 0.7550 (t) REVERT: D 1069 GLU cc_start: 0.6475 (tp30) cc_final: 0.6164 (tm-30) REVERT: D 1202 ASP cc_start: 0.7255 (t70) cc_final: 0.6923 (t0) outliers start: 97 outliers final: 53 residues processed: 358 average time/residue: 0.1054 time to fit residues: 62.4032 Evaluate side-chains 319 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 523 TYR Chi-restraints excluded: chain A residue 609 THR 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 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 613 ILE 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 1134 ILE Chi-restraints excluded: chain B residue 1135 LEU 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 463 MET 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 690 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 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 1057 MET 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 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1058 THR 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 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 187 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 756 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108977 restraints weight = 30288.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109827 restraints weight = 17028.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110403 restraints weight = 13689.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110612 restraints weight = 13129.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110810 restraints weight = 12213.688| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19878 Z= 0.125 Angle : 0.540 9.984 26866 Z= 0.286 Chirality : 0.040 0.176 2998 Planarity : 0.003 0.035 3312 Dihedral : 5.718 84.546 2694 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.02 % Allowed : 16.40 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2460 helix: 1.89 (0.14), residues: 1344 sheet: -1.05 (0.43), residues: 142 loop : -1.61 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 628 TYR 0.025 0.001 TYR C1155 PHE 0.017 0.001 PHE D 438 TRP 0.012 0.001 TRP D1063 HIS 0.011 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (19866) covalent geometry : angle 0.53764 / 0.29 (26842) SS BOND : bond 0.00441 / 0.26 ( 12) SS BOND : angle 1.64235 / 1.13 ( 24) hydrogen bonds : bond 0.03725 / 2.43 ( 1078) hydrogen bonds : angle 3.98984 / 2.76 ( 3138) *********************** 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 374 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 311 time to evaluate : 0.711 Fit side-chains REVERT: A 407 MET cc_start: 0.7908 (mtm) cc_final: 0.7655 (mtt) REVERT: A 642 GLN cc_start: 0.8410 (pp30) cc_final: 0.8131 (pp30) REVERT: B 563 GLN cc_start: 0.5788 (mt0) cc_final: 0.4785 (tm-30) REVERT: B 589 CYS cc_start: 0.6734 (t) cc_final: 0.6515 (t) REVERT: B 1005 ARG cc_start: 0.6380 (tmm-80) cc_final: 0.5794 (mtp-110) REVERT: B 1032 TRP cc_start: 0.8494 (m100) cc_final: 0.8149 (m-10) REVERT: B 1035 SER cc_start: 0.8178 (p) cc_final: 0.7787 (t) REVERT: B 1077 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6411 (ptpt) REVERT: C 414 MET cc_start: 0.7811 (mpt) cc_final: 0.7576 (mtp) REVERT: C 642 GLN cc_start: 0.8429 (pp30) cc_final: 0.8149 (pp30) REVERT: C 742 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7661 (pp) REVERT: C 1095 TYR cc_start: 0.7253 (t80) cc_final: 0.6752 (t80) REVERT: D 467 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8395 (mm) REVERT: D 486 GLU cc_start: 0.7665 (tp30) cc_final: 0.7287 (tp30) REVERT: D 563 GLN cc_start: 0.5670 (mt0) cc_final: 0.4744 (tm-30) REVERT: D 684 ARG cc_start: 0.7821 (pmm150) cc_final: 0.7521 (mtm-85) REVERT: D 705 GLU cc_start: 0.7895 (mp0) cc_final: 0.7654 (mp0) REVERT: D 1032 TRP cc_start: 0.8456 (m100) cc_final: 0.8083 (m-10) REVERT: D 1035 SER cc_start: 0.8038 (p) cc_final: 0.7670 (t) REVERT: D 1069 GLU cc_start: 0.6421 (tp30) cc_final: 0.6119 (tm-30) REVERT: D 1077 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.6683 (ptpp) REVERT: D 1199 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8219 (mmp) REVERT: D 1202 ASP cc_start: 0.7260 (t70) cc_final: 0.6940 (t0) outliers start: 63 outliers final: 40 residues processed: 349 average time/residue: 0.1140 time to fit residues: 65.1830 Evaluate side-chains 328 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1077 LYS Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU 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 527 MET Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 693 VAL 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 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 1149 ILE 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 1058 THR Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1120 CYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1199 MET 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 115 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 231 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 756 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN D 412 HIS ** 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 = 0.3666 r_free = 0.3666 target = 0.138328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108025 restraints weight = 30396.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109085 restraints weight = 16866.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109171 restraints weight = 14020.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109465 restraints weight = 13204.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109608 restraints weight = 12609.345| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19878 Z= 0.143 Angle : 0.544 10.625 26866 Z= 0.288 Chirality : 0.041 0.190 2998 Planarity : 0.003 0.034 3312 Dihedral : 5.659 85.117 2694 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.02 % Allowed : 17.69 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2460 helix: 1.98 (0.14), residues: 1346 sheet: -1.41 (0.42), residues: 152 loop : -1.56 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 715 TYR 0.027 0.001 TYR A1155 PHE 0.014 0.001 PHE D 438 TRP 0.009 0.001 TRP A1063 HIS 0.010 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (19866) covalent geometry : angle 0.54309 / 0.29 (26842) SS BOND : bond 0.00229 / 0.17 ( 12) SS BOND : angle 1.27414 / 0.89 ( 24) hydrogen bonds : bond 0.03771 / 2.45 ( 1078) hydrogen bonds : angle 3.96336 / 2.74 ( 3138) *********************** 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 365 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 302 time to evaluate : 0.503 Fit side-chains REVERT: B 563 GLN cc_start: 0.5754 (mt0) cc_final: 0.4616 (tm-30) REVERT: B 589 CYS cc_start: 0.6759 (t) cc_final: 0.6533 (t) REVERT: B 1005 ARG cc_start: 0.6263 (tmm-80) cc_final: 0.5698 (mtp-110) REVERT: B 1009 MET cc_start: 0.8011 (tpp) cc_final: 0.7692 (tmm) REVERT: B 1032 TRP cc_start: 0.8502 (m100) cc_final: 0.8119 (m-10) REVERT: B 1035 SER cc_start: 0.8219 (p) cc_final: 0.7817 (t) REVERT: B 1069 GLU cc_start: 0.6329 (tp30) cc_final: 0.6052 (tm-30) REVERT: B 1077 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.6461 (ptpt) REVERT: C 414 MET cc_start: 0.7855 (mpt) cc_final: 0.7583 (mtp) REVERT: C 427 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7313 (t0) REVERT: C 742 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7671 (pp) REVERT: C 1095 TYR cc_start: 0.7308 (t80) cc_final: 0.6812 (t80) REVERT: D 467 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8360 (mm) REVERT: D 486 GLU cc_start: 0.7748 (tp30) cc_final: 0.7350 (tp30) REVERT: D 563 GLN cc_start: 0.5595 (mt0) cc_final: 0.4768 (tm-30) REVERT: D 656 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8045 (tmtt) REVERT: D 684 ARG cc_start: 0.7833 (pmm150) cc_final: 0.7538 (mtm-85) REVERT: D 705 GLU cc_start: 0.7915 (mp0) cc_final: 0.7655 (mp0) REVERT: D 1032 TRP cc_start: 0.8472 (m100) cc_final: 0.8076 (m-10) REVERT: D 1035 SER cc_start: 0.8009 (p) cc_final: 0.7630 (t) REVERT: D 1069 GLU cc_start: 0.6460 (tp30) cc_final: 0.6072 (tm-30) REVERT: D 1199 MET cc_start: 0.8422 (mmt) cc_final: 0.8209 (mmp) REVERT: D 1202 ASP cc_start: 0.7368 (t70) cc_final: 0.7045 (t0) outliers start: 63 outliers final: 47 residues processed: 337 average time/residue: 0.1071 time to fit residues: 59.6875 Evaluate side-chains 339 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 514 VAL 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 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 503 MET 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 1116 MET Chi-restraints excluded: chain B residue 1135 LEU 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 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 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 1149 ILE Chi-restraints excluded: chain C residue 1154 VAL 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 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 1058 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 181 optimal weight: 0.0980 chunk 79 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109442 restraints weight = 30505.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112110 restraints weight = 20043.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112671 restraints weight = 13834.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112701 restraints weight = 12412.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113195 restraints weight = 11454.426| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19878 Z= 0.123 Angle : 0.527 11.389 26866 Z= 0.278 Chirality : 0.040 0.187 2998 Planarity : 0.003 0.032 3312 Dihedral : 5.515 83.990 2694 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.07 % Allowed : 17.98 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.17), residues: 2460 helix: 2.08 (0.14), residues: 1352 sheet: -1.46 (0.41), residues: 152 loop : -1.49 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 715 TYR 0.024 0.001 TYR A1155 PHE 0.015 0.001 PHE D 438 TRP 0.011 0.001 TRP D1063 HIS 0.010 0.001 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (19866) covalent geometry : angle 0.52673 / 0.28 (26842) SS BOND : bond 0.00147 / 0.10 ( 12) SS BOND : angle 0.94860 / 0.66 ( 24) hydrogen bonds : bond 0.03559 / 2.32 ( 1078) hydrogen bonds : angle 3.86821 / 2.67 ( 3138) *********************** 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 382 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 318 time to evaluate : 0.735 Fit side-chains REVERT: A 450 TYR cc_start: 0.8188 (m-80) cc_final: 0.7821 (m-80) REVERT: A 642 GLN cc_start: 0.8356 (pp30) cc_final: 0.8123 (pp30) REVERT: B 486 GLU cc_start: 0.7792 (tp30) cc_final: 0.7463 (tp30) REVERT: B 563 GLN cc_start: 0.5830 (mt0) cc_final: 0.4838 (tm-30) REVERT: B 589 CYS cc_start: 0.6709 (t) cc_final: 0.6439 (t) REVERT: B 1005 ARG cc_start: 0.6048 (tmm-80) cc_final: 0.5615 (mtp-110) REVERT: B 1032 TRP cc_start: 0.8466 (m100) cc_final: 0.8116 (m-10) REVERT: B 1035 SER cc_start: 0.8258 (p) cc_final: 0.7837 (t) REVERT: B 1077 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6505 (ptpt) REVERT: C 414 MET cc_start: 0.7789 (mpt) cc_final: 0.7523 (mtp) REVERT: C 642 GLN cc_start: 0.8382 (pp30) cc_final: 0.8144 (pp30) REVERT: C 1095 TYR cc_start: 0.7298 (t80) cc_final: 0.6824 (t80) REVERT: D 467 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8446 (mm) REVERT: D 486 GLU cc_start: 0.7727 (tp30) cc_final: 0.7301 (tp30) REVERT: D 563 GLN cc_start: 0.5766 (mt0) cc_final: 0.4952 (tm-30) REVERT: D 656 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8068 (tmtt) REVERT: D 684 ARG cc_start: 0.7813 (pmm150) cc_final: 0.7526 (mtm-85) REVERT: D 705 GLU cc_start: 0.7893 (mp0) cc_final: 0.7662 (mp0) REVERT: D 1032 TRP cc_start: 0.8449 (m100) cc_final: 0.8083 (m-10) REVERT: D 1035 SER cc_start: 0.8093 (p) cc_final: 0.7719 (t) REVERT: D 1069 GLU cc_start: 0.6396 (tp30) cc_final: 0.6123 (tm-30) REVERT: D 1202 ASP cc_start: 0.7327 (t70) cc_final: 0.7005 (t0) outliers start: 64 outliers final: 48 residues processed: 355 average time/residue: 0.1082 time to fit residues: 62.7630 Evaluate side-chains 337 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 287 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 400 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 543 VAL 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 1044 VAL Chi-restraints excluded: chain B residue 1077 LYS Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 395 VAL 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 690 VAL 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 C residue 1184 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 1058 THR Chi-restraints excluded: chain D residue 1120 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 229 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 714 GLN D1008 GLN ** D1131 HIS ** 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 = 0.3590 r_free = 0.3590 target = 0.132508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102729 restraints weight = 31253.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.104180 restraints weight = 23094.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104857 restraints weight = 16229.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105084 restraints weight = 13916.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105405 restraints weight = 12737.548| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 19878 Z= 0.365 Angle : 0.733 12.890 26866 Z= 0.388 Chirality : 0.049 0.236 2998 Planarity : 0.005 0.045 3312 Dihedral : 6.323 92.709 2694 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.79 % Allowed : 18.46 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2460 helix: 1.42 (0.14), residues: 1324 sheet: -1.33 (0.44), residues: 142 loop : -1.67 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1036 TYR 0.029 0.002 TYR C 523 PHE 0.023 0.003 PHE A1115 TRP 0.015 0.002 TRP C 578 HIS 0.011 0.002 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.37 (19866) covalent geometry : angle 0.73149 / 0.39 (26842) SS BOND : bond 0.00505 / 0.38 ( 12) SS BOND : angle 1.62986 / 1.14 ( 24) hydrogen bonds : bond 0.04941 / 3.21 ( 1078) hydrogen bonds : angle 4.51479 / 3.13 ( 3138) *********************** 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 365 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 286 time to evaluate : 0.715 Fit side-chains REVERT: A 450 TYR cc_start: 0.8313 (m-80) cc_final: 0.7845 (m-80) REVERT: B 1005 ARG cc_start: 0.6437 (tmm-80) cc_final: 0.5872 (mtm110) REVERT: B 1032 TRP cc_start: 0.8497 (m100) cc_final: 0.8124 (m-10) REVERT: B 1035 SER cc_start: 0.8157 (p) cc_final: 0.7771 (t) REVERT: B 1072 PHE cc_start: 0.7299 (m-80) cc_final: 0.7082 (m-80) REVERT: B 1077 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6705 (ptpt) REVERT: C 414 MET cc_start: 0.7742 (mpt) cc_final: 0.7531 (mtp) REVERT: C 1095 TYR cc_start: 0.7330 (t80) cc_final: 0.6758 (t80) REVERT: D 656 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8129 (tmtt) REVERT: D 684 ARG cc_start: 0.7890 (pmm150) cc_final: 0.7565 (mtm-85) REVERT: D 705 GLU cc_start: 0.7947 (mp0) cc_final: 0.7684 (mp0) REVERT: D 1032 TRP cc_start: 0.8487 (m100) cc_final: 0.8100 (m-10) REVERT: D 1035 SER cc_start: 0.8061 (p) cc_final: 0.7664 (t) REVERT: D 1077 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.6826 (ptpt) REVERT: D 1202 ASP cc_start: 0.7386 (t70) cc_final: 0.7080 (t0) outliers start: 79 outliers final: 62 residues processed: 337 average time/residue: 0.1106 time to fit residues: 61.8837 Evaluate side-chains 325 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 609 THR 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 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 613 ILE 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 1044 VAL Chi-restraints excluded: chain B residue 1077 LYS Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU 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 395 VAL 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 690 VAL Chi-restraints excluded: chain C residue 693 VAL 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 1057 MET 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 1152 ILE Chi-restraints excluded: chain C residue 1154 VAL Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 813 GLU Chi-restraints excluded: chain D residue 1058 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 168 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS ** D1131 HIS ** 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 = 0.3667 r_free = 0.3667 target = 0.138596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108769 restraints weight = 30359.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109478 restraints weight = 18015.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110376 restraints weight = 15214.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110912 restraints weight = 13412.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111137 restraints weight = 12964.874| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19878 Z= 0.125 Angle : 0.562 13.170 26866 Z= 0.295 Chirality : 0.041 0.206 2998 Planarity : 0.003 0.035 3312 Dihedral : 5.657 84.430 2694 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.54 % Allowed : 20.04 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2460 helix: 2.01 (0.14), residues: 1334 sheet: -1.35 (0.43), residues: 142 loop : -1.57 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1036 TYR 0.027 0.001 TYR A1155 PHE 0.013 0.001 PHE D 438 TRP 0.015 0.001 TRP D1063 HIS 0.010 0.001 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (19866) covalent geometry : angle 0.56115 / 0.30 (26842) SS BOND : bond 0.00154 / 0.11 ( 12) SS BOND : angle 0.91622 / 0.63 ( 24) hydrogen bonds : bond 0.03694 / 2.41 ( 1078) hydrogen bonds : angle 3.98623 / 2.75 ( 3138) *********************** 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 358 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 0.714 Fit side-chains REVERT: A 450 TYR cc_start: 0.8139 (m-80) cc_final: 0.7786 (m-80) REVERT: B 563 GLN cc_start: 0.5821 (mt0) cc_final: 0.4767 (tm-30) REVERT: B 589 CYS cc_start: 0.6683 (t) cc_final: 0.6413 (t) REVERT: B 1005 ARG cc_start: 0.6255 (tmm-80) cc_final: 0.5759 (mtp-110) REVERT: B 1032 TRP cc_start: 0.8474 (m100) cc_final: 0.8127 (m-10) REVERT: B 1035 SER cc_start: 0.8108 (p) cc_final: 0.7729 (t) REVERT: B 1077 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6474 (ptpt) REVERT: C 414 MET cc_start: 0.7823 (mpt) cc_final: 0.7592 (mtp) REVERT: C 1063 TRP cc_start: 0.7932 (m-90) cc_final: 0.7657 (m-90) REVERT: C 1095 TYR cc_start: 0.7396 (t80) cc_final: 0.6846 (t80) REVERT: D 563 GLN cc_start: 0.5916 (mt0) cc_final: 0.4887 (tm-30) REVERT: D 656 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8032 (tmtt) REVERT: D 684 ARG cc_start: 0.7850 (pmm150) cc_final: 0.7542 (mtm-85) REVERT: D 705 GLU cc_start: 0.7881 (mp0) cc_final: 0.7665 (mp0) REVERT: D 1032 TRP cc_start: 0.8472 (m100) cc_final: 0.8124 (m-10) REVERT: D 1035 SER cc_start: 0.8048 (p) cc_final: 0.7677 (t) REVERT: D 1077 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.6615 (ptpp) REVERT: D 1202 ASP cc_start: 0.7398 (t70) cc_final: 0.7051 (t0) outliers start: 53 outliers final: 47 residues processed: 335 average time/residue: 0.1061 time to fit residues: 58.5472 Evaluate side-chains 338 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 289 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 543 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 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 1191 MET Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 543 VAL 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 1044 VAL Chi-restraints excluded: chain B residue 1077 LYS Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU 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 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 690 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 C residue 1154 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 813 GLU Chi-restraints excluded: chain D residue 1058 THR 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 235 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 57 optimal weight: 0.0770 chunk 140 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS 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 = 0.139713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109874 restraints weight = 30536.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112637 restraints weight = 19881.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113315 restraints weight = 13954.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113163 restraints weight = 12137.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113230 restraints weight = 11246.467| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19878 Z= 0.120 Angle : 0.553 13.314 26866 Z= 0.289 Chirality : 0.041 0.197 2998 Planarity : 0.003 0.033 3312 Dihedral : 5.524 85.439 2694 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.16 % Allowed : 20.71 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2460 helix: 2.17 (0.14), residues: 1340 sheet: -1.30 (0.43), residues: 142 loop : -1.50 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1036 TYR 0.026 0.001 TYR A1155 PHE 0.014 0.001 PHE D 438 TRP 0.013 0.001 TRP D1063 HIS 0.012 0.001 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19866) covalent geometry : angle 0.55210 / 0.29 (26842) SS BOND : bond 0.00166 / 0.12 ( 12) SS BOND : angle 0.91855 / 0.62 ( 24) hydrogen bonds : bond 0.03531 / 2.30 ( 1078) hydrogen bonds : angle 3.87666 / 2.67 ( 3138) ********************** 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 343 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 298 time to evaluate : 0.560 Fit side-chains REVERT: A 450 TYR cc_start: 0.8186 (m-80) cc_final: 0.7800 (m-80) REVERT: A 1116 MET cc_start: 0.8703 (tpt) cc_final: 0.8434 (tpt) REVERT: B 486 GLU cc_start: 0.7805 (tp30) cc_final: 0.7485 (tp30) REVERT: B 563 GLN cc_start: 0.5821 (mt0) cc_final: 0.4813 (tm-30) REVERT: B 589 CYS cc_start: 0.6698 (t) cc_final: 0.6397 (t) REVERT: B 1005 ARG cc_start: 0.6172 (tmm-80) cc_final: 0.5819 (mtm110) REVERT: B 1032 TRP cc_start: 0.8455 (m100) cc_final: 0.8128 (m-10) REVERT: B 1035 SER cc_start: 0.8191 (p) cc_final: 0.7782 (t) REVERT: C 414 MET cc_start: 0.7753 (mpt) cc_final: 0.7508 (mtp) REVERT: C 1063 TRP cc_start: 0.7949 (m-90) cc_final: 0.7738 (m-90) REVERT: C 1095 TYR cc_start: 0.7405 (t80) cc_final: 0.6875 (t80) REVERT: D 563 GLN cc_start: 0.5895 (mt0) cc_final: 0.4865 (tm-30) REVERT: D 656 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8054 (tmtt) REVERT: D 684 ARG cc_start: 0.7823 (pmm150) cc_final: 0.7524 (mtm-85) REVERT: D 705 GLU cc_start: 0.7876 (mp0) cc_final: 0.7669 (mp0) REVERT: D 1032 TRP cc_start: 0.8435 (m100) cc_final: 0.8087 (m-10) REVERT: D 1035 SER cc_start: 0.8085 (p) cc_final: 0.7737 (t) REVERT: D 1077 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.6629 (ptpp) REVERT: D 1202 ASP cc_start: 0.7343 (t70) cc_final: 0.7003 (t0) outliers start: 45 outliers final: 41 residues processed: 324 average time/residue: 0.1079 time to fit residues: 57.2635 Evaluate side-chains 333 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 543 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 1009 MET 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 B residue 445 VAL Chi-restraints excluded: chain B residue 543 VAL 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 1044 VAL Chi-restraints excluded: chain B residue 1135 LEU 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 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 690 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 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 1058 THR 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 80 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 HIS B 791 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110337 restraints weight = 30516.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111862 restraints weight = 19208.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112663 restraints weight = 14745.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112927 restraints weight = 13043.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112911 restraints weight = 12540.570| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19878 Z= 0.119 Angle : 0.553 13.260 26866 Z= 0.288 Chirality : 0.041 0.196 2998 Planarity : 0.003 0.032 3312 Dihedral : 5.435 85.336 2694 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.59 % Allowed : 20.33 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2460 helix: 2.24 (0.14), residues: 1342 sheet: -1.27 (0.43), residues: 142 loop : -1.49 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 715 TYR 0.025 0.001 TYR A1155 PHE 0.019 0.001 PHE B 438 TRP 0.011 0.001 TRP D1063 HIS 0.012 0.001 HIS D 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (19866) covalent geometry : angle 0.55270 / 0.29 (26842) SS BOND : bond 0.00212 / 0.15 ( 12) SS BOND : angle 0.85983 / 0.59 ( 24) hydrogen bonds : bond 0.03474 / 2.27 ( 1078) hydrogen bonds : angle 3.83989 / 2.64 ( 3138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2689.52 seconds wall clock time: 47 minutes 33.34 seconds (2853.34 seconds total)