Starting phenix.real_space_refine on Thu Mar 5 05:15:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnl_26013/03_2026/7tnl_26013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnl_26013/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnl_26013/03_2026/7tnl_26013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnl_26013/03_2026/7tnl_26013.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnl_26013/03_2026/7tnl_26013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnl_26013/03_2026/7tnl_26013.cif" } 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-5986/lib/python3.9/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: 3.74, per 1000 atoms: 0.19 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: 1.68 Conformation dependent library (CDL) restraints added in 811.2 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: 0.45 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: 3.67 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5667 1.34 - 1.46: 3896 1.46 - 1.57: 10075 1.57 - 1.69: 8 1.69 - 1.81: 220 Bond restraints: 19866 Sorted by residual: bond pdb=" CB ILE A 525 " pdb=" CG2 ILE A 525 " ideal model delta sigma weight residual 1.521 1.389 0.132 3.30e-02 9.18e+02 1.60e+01 bond pdb=" CB ILE C 525 " pdb=" CG2 ILE C 525 " ideal model delta sigma weight residual 1.521 1.390 0.131 3.30e-02 9.18e+02 1.58e+01 bond pdb=" N GLU A1046 " pdb=" CA GLU A1046 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.17e-02 7.31e+03 8.13e+00 bond pdb=" N GLU C1046 " pdb=" CA GLU C1046 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.17e-02 7.31e+03 7.98e+00 bond pdb=" CG1 ILE C 525 " pdb=" CD1 ILE C 525 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.16e+00 ... (remaining 19861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 25858 2.38 - 4.77: 815 4.77 - 7.15: 131 7.15 - 9.54: 30 9.54 - 11.92: 8 Bond angle restraints: 26842 Sorted by residual: angle pdb=" C GLU D1054 " pdb=" N GLU D1055 " pdb=" CA GLU D1055 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C GLU B1054 " pdb=" N GLU B1055 " pdb=" CA GLU B1055 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C SER B1045 " pdb=" N GLU B1046 " pdb=" CA GLU B1046 " ideal model delta sigma weight residual 121.19 130.84 -9.65 1.59e+00 3.96e-01 3.68e+01 angle pdb=" C SER D1045 " pdb=" N GLU D1046 " pdb=" CA GLU D1046 " ideal model delta sigma weight residual 121.19 130.82 -9.63 1.59e+00 3.96e-01 3.67e+01 angle pdb=" C SER C1045 " pdb=" N GLU C1046 " pdb=" CA GLU C1046 " ideal model delta sigma weight residual 121.19 130.03 -8.84 1.59e+00 3.96e-01 3.09e+01 ... (remaining 26837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 11406 24.11 - 48.23: 346 48.23 - 72.34: 28 72.34 - 96.45: 6 96.45 - 120.57: 10 Dihedral angle restraints: 11796 sinusoidal: 4666 harmonic: 7130 Sorted by residual: dihedral pdb=" CA GLU A 627 " pdb=" C GLU A 627 " pdb=" N ARG A 628 " pdb=" CA ARG A 628 " ideal model delta harmonic sigma weight residual 180.00 138.84 41.16 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA GLU C 627 " pdb=" C GLU C 627 " pdb=" N ARG C 628 " pdb=" CA ARG C 628 " ideal model delta harmonic sigma weight residual 180.00 138.85 41.15 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA GLU B1054 " pdb=" C GLU B1054 " pdb=" N GLU B1055 " pdb=" CA GLU B1055 " ideal model delta harmonic sigma weight residual 180.00 142.19 37.81 0 5.00e+00 4.00e-02 5.72e+01 ... (remaining 11793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2471 0.071 - 0.143: 440 0.143 - 0.214: 71 0.214 - 0.285: 14 0.285 - 0.356: 2 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU A1114 " pdb=" CB LEU A1114 " pdb=" CD1 LEU A1114 " pdb=" CD2 LEU A1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CG LEU C1114 " pdb=" CB LEU C1114 " pdb=" CD1 LEU C1114 " pdb=" CD2 LEU C1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB THR C1065 " pdb=" CA THR C1065 " pdb=" OG1 THR C1065 " pdb=" CG2 THR C1065 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2995 not shown) Planarity restraints: 3312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 627 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C GLU C 627 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU C 627 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG C 628 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 627 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C GLU A 627 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 627 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 628 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO C 520 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.032 5.00e-02 4.00e+02 ... (remaining 3309 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4701 2.78 - 3.31: 17964 3.31 - 3.84: 31508 3.84 - 4.37: 37019 4.37 - 4.90: 64299 Nonbonded interactions: 155491 Sorted by model distance: nonbonded pdb=" OD1 ASP C1047 " pdb=" OG SER C1050 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASP A1047 " pdb=" OG SER A1050 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR C 655 " pdb=" OE2 GLU C 705 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR A 655 " pdb=" OE2 GLU A 705 " model vdw 2.282 3.040 nonbonded pdb=" OG SER A 597 " pdb=" O ALA B 806 " model vdw 2.315 3.040 ... (remaining 155486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.150 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.132 19878 Z= 0.385 Angle : 1.030 11.924 26866 Z= 0.556 Chirality : 0.059 0.356 2998 Planarity : 0.007 0.057 3312 Dihedral : 11.859 120.568 7212 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.12 % Rotamer: Outliers : 0.38 % Allowed : 5.75 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z 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 covalent geometry : bond 0.00921 (19866) covalent geometry : angle 1.02879 (26842) SS BOND : bond 0.01176 ( 12) SS BOND : angle 1.90627 ( 24) hydrogen bonds : bond 0.27055 ( 1078) hydrogen bonds : angle 8.99511 ( 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 : 0.625 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: 0.1426 time to fit residues: 118.8473 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 : 0.761 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 714 GLN A 756 GLN A1206 GLN B 791 ASN B1071 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C 756 GLN C1131 HIS C1206 GLN D 791 ASN D1071 ASN ** D1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108988 restraints weight = 30495.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111317 restraints weight = 18029.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111928 restraints weight = 13889.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112150 restraints weight = 12355.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112135 restraints weight = 11710.492| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19878 Z= 0.159 Angle : 0.611 9.713 26866 Z= 0.324 Chirality : 0.042 0.215 2998 Planarity : 0.005 0.043 3312 Dihedral : 8.732 103.796 2790 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.68 % Allowed : 11.84 % Favored : 85.47 % 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: -0.07 (0.12), residues: 1330 sheet: -1.30 (0.39), residues: 142 loop : -1.80 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D1036 TYR 0.024 0.001 TYR C 523 PHE 0.021 0.002 PHE D1200 TRP 0.013 0.002 TRP D 767 HIS 0.017 0.002 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00363 (19866) covalent geometry : angle 0.60978 (26842) SS BOND : bond 0.00323 ( 12) SS BOND : angle 1.36978 ( 24) hydrogen bonds : bond 0.04724 ( 1078) hydrogen bonds : angle 4.50588 ( 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 440 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 384 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7638 (mpt) cc_final: 0.7361 (mtp) REVERT: A 742 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7254 (pp) REVERT: A 1025 ILE cc_start: 0.8365 (mm) cc_final: 0.8147 (mm) REVERT: A 1126 PHE cc_start: 0.7568 (t80) cc_final: 0.7309 (m-80) REVERT: B 563 GLN cc_start: 0.5449 (mt0) cc_final: 0.4714 (tm-30) REVERT: B 642 GLN cc_start: 0.8207 (pp30) cc_final: 0.7829 (pp30) REVERT: B 656 LYS cc_start: 0.8480 (tttt) cc_final: 0.8192 (tmtt) REVERT: B 684 ARG cc_start: 0.7841 (pmm150) cc_final: 0.7634 (mtm-85) REVERT: B 1009 MET cc_start: 0.8037 (tpp) cc_final: 0.7644 (tmm) REVERT: B 1032 TRP cc_start: 0.8448 (m100) cc_final: 0.8095 (m-10) REVERT: B 1035 SER cc_start: 0.8214 (p) cc_final: 0.7842 (t) REVERT: B 1119 LEU cc_start: 0.7615 (tt) cc_final: 0.7119 (tp) REVERT: B 1199 MET cc_start: 0.7988 (mmm) cc_final: 0.7773 (mmt) REVERT: C 414 MET cc_start: 0.7687 (mpt) cc_final: 0.7479 (mtp) REVERT: C 642 GLN cc_start: 0.8344 (pp30) cc_final: 0.8047 (pp30) REVERT: C 742 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7454 (pp) REVERT: C 788 SER cc_start: 0.8640 (m) cc_final: 0.8427 (t) REVERT: C 813 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6672 (tp30) REVERT: C 1095 TYR cc_start: 0.7198 (t80) cc_final: 0.6659 (t80) REVERT: C 1150 ILE cc_start: 0.9017 (tp) cc_final: 0.8813 (tp) REVERT: D 684 ARG cc_start: 0.7762 (pmm150) cc_final: 0.7439 (mtm-85) REVERT: D 1035 SER cc_start: 0.8106 (p) cc_final: 0.7724 (t) REVERT: D 1202 ASP cc_start: 0.7140 (t70) cc_final: 0.6881 (t0) outliers start: 56 outliers final: 25 residues processed: 426 average time/residue: 0.1183 time to fit residues: 79.0974 Evaluate side-chains 320 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 1121 ILE 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 1184 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 1014 VAL Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 106 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 71 optimal weight: 0.0070 chunk 166 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN C1131 HIS ** 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 = 0.3669 r_free = 0.3669 target = 0.138473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108331 restraints weight = 30560.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110298 restraints weight = 19023.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111058 restraints weight = 14353.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111110 restraints weight = 12685.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111153 restraints weight = 11676.441| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19878 Z= 0.153 Angle : 0.565 8.198 26866 Z= 0.298 Chirality : 0.041 0.185 2998 Planarity : 0.004 0.036 3312 Dihedral : 8.131 95.518 2790 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.69 % Allowed : 14.38 % Favored : 81.93 % 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: 0.06 (0.16), residues: 2460 helix: 1.34 (0.14), residues: 1330 sheet: -1.06 (0.41), residues: 142 loop : -1.65 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 453 TYR 0.022 0.001 TYR C 523 PHE 0.013 0.002 PHE B1141 TRP 0.014 0.001 TRP B1063 HIS 0.015 0.002 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00354 (19866) covalent geometry : angle 0.56477 (26842) SS BOND : bond 0.00370 ( 12) SS BOND : angle 0.92677 ( 24) hydrogen bonds : bond 0.04164 ( 1078) hydrogen bonds : angle 4.14312 ( 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 394 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 317 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 642 GLN cc_start: 0.8492 (pp30) cc_final: 0.8152 (pp30) REVERT: A 742 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7385 (pp) REVERT: A 1126 PHE cc_start: 0.7430 (t80) cc_final: 0.7208 (m-80) REVERT: B 563 GLN cc_start: 0.5468 (mt0) cc_final: 0.4779 (tm-30) REVERT: B 642 GLN cc_start: 0.8224 (pp30) cc_final: 0.7917 (pp30) REVERT: B 656 LYS cc_start: 0.8501 (tttt) cc_final: 0.8291 (tmtt) REVERT: B 1005 ARG cc_start: 0.6368 (tmm-80) cc_final: 0.5819 (mtm110) REVERT: B 1009 MET cc_start: 0.7963 (tpp) cc_final: 0.7589 (tmm) REVERT: B 1032 TRP cc_start: 0.8452 (m100) cc_final: 0.8082 (m-10) REVERT: B 1035 SER cc_start: 0.8355 (p) cc_final: 0.7974 (t) REVERT: B 1113 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8573 (mt) REVERT: B 1199 MET cc_start: 0.8058 (mmm) cc_final: 0.7816 (mmt) REVERT: C 414 MET cc_start: 0.7725 (mpt) cc_final: 0.7519 (mtp) REVERT: C 642 GLN cc_start: 0.8411 (pp30) cc_final: 0.8112 (pp30) REVERT: C 742 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7442 (pp) REVERT: C 813 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6667 (tp30) REVERT: C 1095 TYR cc_start: 0.7210 (t80) cc_final: 0.6713 (t80) REVERT: C 1198 HIS cc_start: 0.8074 (m-70) cc_final: 0.7818 (m-70) REVERT: D 467 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8518 (mm) REVERT: D 486 GLU cc_start: 0.7679 (tp30) cc_final: 0.7433 (tp30) REVERT: D 684 ARG cc_start: 0.7806 (pmm150) cc_final: 0.7501 (mtm-85) REVERT: D 1035 SER cc_start: 0.8218 (p) cc_final: 0.7804 (t) REVERT: D 1077 LYS cc_start: 0.8022 (tttt) cc_final: 0.6738 (ptpp) REVERT: D 1202 ASP cc_start: 0.7157 (t70) cc_final: 0.6705 (t0) outliers start: 77 outliers final: 37 residues processed: 370 average time/residue: 0.1067 time to fit residues: 64.8050 Evaluate side-chains 322 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1113 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 523 TYR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 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 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 1187 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 165 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 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: 0.0770 chunk 11 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 69 optimal weight: 0.0270 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109685 restraints weight = 30632.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111778 restraints weight = 18771.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112131 restraints weight = 13580.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112413 restraints weight = 12979.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112562 restraints weight = 11874.158| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3674 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= 0.127 Angle : 0.532 8.004 26866 Z= 0.279 Chirality : 0.041 0.175 2998 Planarity : 0.003 0.035 3312 Dihedral : 7.657 91.501 2790 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.07 % Allowed : 15.00 % Favored : 81.93 % 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: 0.56 (0.17), residues: 2460 helix: 1.89 (0.14), residues: 1330 sheet: -1.28 (0.40), residues: 152 loop : -1.58 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1203 TYR 0.026 0.001 TYR C1155 PHE 0.018 0.001 PHE D 438 TRP 0.010 0.001 TRP B1063 HIS 0.012 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00292 (19866) covalent geometry : angle 0.53168 (26842) SS BOND : bond 0.00173 ( 12) SS BOND : angle 0.79316 ( 24) hydrogen bonds : bond 0.03711 ( 1078) hydrogen bonds : angle 3.94324 ( 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 381 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 317 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 642 GLN cc_start: 0.8472 (pp30) cc_final: 0.8269 (pp30) REVERT: A 1126 PHE cc_start: 0.7424 (t80) cc_final: 0.7206 (m-80) REVERT: B 563 GLN cc_start: 0.5526 (mt0) cc_final: 0.4843 (tm-30) REVERT: B 589 CYS cc_start: 0.6756 (t) cc_final: 0.6442 (t) REVERT: B 642 GLN cc_start: 0.8201 (pp30) cc_final: 0.7977 (pp30) REVERT: B 656 LYS cc_start: 0.8492 (tttt) cc_final: 0.8190 (ttmt) REVERT: B 1005 ARG cc_start: 0.6306 (tmm-80) cc_final: 0.5807 (mtp-110) REVERT: B 1009 MET cc_start: 0.7970 (tpp) cc_final: 0.7654 (tmm) REVERT: B 1032 TRP cc_start: 0.8442 (m100) cc_final: 0.8086 (m-10) REVERT: B 1035 SER cc_start: 0.8264 (p) cc_final: 0.7846 (t) REVERT: B 1077 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6465 (ptpt) REVERT: B 1113 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 414 MET cc_start: 0.7798 (mpt) cc_final: 0.7553 (mtp) REVERT: C 642 GLN cc_start: 0.8371 (pp30) cc_final: 0.8116 (pp30) REVERT: C 742 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7487 (pp) REVERT: C 819 ARG cc_start: 0.6029 (ppp80) cc_final: 0.5720 (ttm-80) REVERT: C 1095 TYR cc_start: 0.7251 (t80) cc_final: 0.6779 (t80) REVERT: C 1127 TYR cc_start: 0.6919 (t80) cc_final: 0.6704 (t80) REVERT: C 1198 HIS cc_start: 0.8137 (m-70) cc_final: 0.7927 (m-70) REVERT: D 467 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8527 (mm) REVERT: D 486 GLU cc_start: 0.7733 (tp30) cc_final: 0.7417 (tp30) REVERT: D 684 ARG cc_start: 0.7803 (pmm150) cc_final: 0.7504 (mtm-85) REVERT: D 705 GLU cc_start: 0.7864 (mp0) cc_final: 0.7629 (mp0) REVERT: D 1032 TRP cc_start: 0.8344 (m100) cc_final: 0.7989 (m-10) REVERT: D 1035 SER cc_start: 0.8212 (p) cc_final: 0.7774 (t) REVERT: D 1069 GLU cc_start: 0.6391 (tp30) cc_final: 0.6147 (tm-30) REVERT: D 1077 LYS cc_start: 0.7947 (tttt) cc_final: 0.6690 (ptpp) REVERT: D 1202 ASP cc_start: 0.7128 (t70) cc_final: 0.6691 (t0) outliers start: 64 outliers final: 37 residues processed: 356 average time/residue: 0.1137 time to fit residues: 65.8536 Evaluate side-chains 327 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 1077 LYS Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain B residue 596 LEU 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 1077 LYS Chi-restraints excluded: chain B residue 1113 LEU 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 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 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 467 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 813 GLU Chi-restraints excluded: chain D residue 1185 SER 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: 4.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 93 optimal weight: 0.0060 chunk 5 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103379 restraints weight = 30694.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106444 restraints weight = 17534.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108287 restraints weight = 12983.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109043 restraints weight = 11079.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109867 restraints weight = 10285.109| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19878 Z= 0.210 Angle : 0.600 8.780 26866 Z= 0.316 Chirality : 0.043 0.206 2998 Planarity : 0.004 0.036 3312 Dihedral : 7.733 92.598 2790 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.98 % Allowed : 15.15 % Favored : 80.87 % 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: 0.43 (0.17), residues: 2460 helix: 1.79 (0.14), residues: 1330 sheet: -1.31 (0.41), residues: 152 loop : -1.65 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 715 TYR 0.025 0.001 TYR C 523 PHE 0.018 0.002 PHE D1140 TRP 0.009 0.002 TRP C1063 HIS 0.010 0.002 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00501 (19866) covalent geometry : angle 0.59948 (26842) SS BOND : bond 0.00393 ( 12) SS BOND : angle 0.94905 ( 24) hydrogen bonds : bond 0.04257 ( 1078) hydrogen bonds : angle 4.16619 ( 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 377 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 294 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8051 (mtm) cc_final: 0.7841 (mtt) REVERT: B 563 GLN cc_start: 0.5737 (mt0) cc_final: 0.4963 (tm-30) REVERT: B 642 GLN cc_start: 0.8345 (pp30) cc_final: 0.8121 (pp30) REVERT: B 656 LYS cc_start: 0.8555 (tttt) cc_final: 0.8217 (ttmt) REVERT: B 705 GLU cc_start: 0.7900 (mp0) cc_final: 0.7653 (mp0) REVERT: B 1005 ARG cc_start: 0.6407 (tmm-80) cc_final: 0.5842 (mtp-110) REVERT: B 1009 MET cc_start: 0.7900 (tpp) cc_final: 0.7578 (tmm) REVERT: B 1032 TRP cc_start: 0.8510 (m100) cc_final: 0.8129 (m-10) REVERT: B 1035 SER cc_start: 0.8183 (p) cc_final: 0.7812 (t) REVERT: C 407 MET cc_start: 0.8288 (mtm) cc_final: 0.7917 (mtm) REVERT: C 642 GLN cc_start: 0.8361 (pp30) cc_final: 0.8151 (pp30) REVERT: C 742 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7615 (pp) REVERT: C 1023 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8758 (tpt) REVERT: C 1095 TYR cc_start: 0.7300 (t80) cc_final: 0.6797 (t80) REVERT: D 407 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8242 (mtp) REVERT: D 467 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8573 (mm) REVERT: D 647 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: D 684 ARG cc_start: 0.7844 (pmm150) cc_final: 0.7531 (mtm-85) REVERT: D 705 GLU cc_start: 0.7919 (mp0) cc_final: 0.7655 (mp0) REVERT: D 1032 TRP cc_start: 0.8461 (m100) cc_final: 0.8099 (m-10) REVERT: D 1035 SER cc_start: 0.8073 (p) cc_final: 0.7702 (t) REVERT: D 1055 GLU cc_start: 0.4987 (OUTLIER) cc_final: 0.4728 (mm-30) REVERT: D 1069 GLU cc_start: 0.6347 (tp30) cc_final: 0.6088 (tm-30) REVERT: D 1077 LYS cc_start: 0.7878 (tttt) cc_final: 0.6594 (ptpp) REVERT: D 1202 ASP cc_start: 0.7210 (t70) cc_final: 0.6897 (t0) outliers start: 83 outliers final: 53 residues processed: 350 average time/residue: 0.1080 time to fit residues: 62.7780 Evaluate side-chains 328 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 269 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU 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 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 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 1023 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 1184 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 467 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 813 GLU Chi-restraints excluded: chain D residue 1055 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 115 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 189 optimal weight: 0.7980 chunk 230 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106155 restraints weight = 30563.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107197 restraints weight = 16743.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107675 restraints weight = 13833.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107838 restraints weight = 12940.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108229 restraints weight = 12255.303| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19878 Z= 0.190 Angle : 0.584 8.433 26866 Z= 0.307 Chirality : 0.043 0.196 2998 Planarity : 0.003 0.036 3312 Dihedral : 7.465 89.648 2790 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.88 % Allowed : 16.78 % Favored : 79.34 % 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: 0.45 (0.17), residues: 2460 helix: 1.77 (0.14), residues: 1344 sheet: -1.13 (0.44), residues: 142 loop : -1.67 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1203 TYR 0.028 0.001 TYR A1155 PHE 0.013 0.002 PHE C 495 TRP 0.011 0.001 TRP B1063 HIS 0.009 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00453 (19866) covalent geometry : angle 0.58146 (26842) SS BOND : bond 0.00323 ( 12) SS BOND : angle 1.77273 ( 24) hydrogen bonds : bond 0.04049 ( 1078) hydrogen bonds : angle 4.12459 ( 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 375 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 294 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 642 GLN cc_start: 0.8392 (pp30) cc_final: 0.8135 (pp30) REVERT: B 647 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: B 656 LYS cc_start: 0.8578 (tttt) cc_final: 0.8353 (tmtt) REVERT: B 1005 ARG cc_start: 0.6451 (tmm-80) cc_final: 0.5882 (mtp-110) REVERT: B 1009 MET cc_start: 0.7943 (tpp) cc_final: 0.7600 (tmm) REVERT: B 1032 TRP cc_start: 0.8495 (m100) cc_final: 0.8118 (m-10) REVERT: B 1035 SER cc_start: 0.8190 (p) cc_final: 0.7820 (t) REVERT: C 407 MET cc_start: 0.8265 (mtm) cc_final: 0.8052 (mtm) REVERT: C 642 GLN cc_start: 0.8416 (pp30) cc_final: 0.8185 (pp30) REVERT: C 1023 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8750 (tpt) REVERT: C 1063 TRP cc_start: 0.7985 (m-90) cc_final: 0.7603 (m-90) REVERT: C 1095 TYR cc_start: 0.7361 (t80) cc_final: 0.6836 (t80) REVERT: D 407 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8266 (mtp) REVERT: D 467 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8454 (mm) REVERT: D 656 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8045 (tmtt) REVERT: D 684 ARG cc_start: 0.7864 (pmm150) cc_final: 0.7542 (mtm-85) REVERT: D 705 GLU cc_start: 0.7866 (mp0) cc_final: 0.7624 (mp0) REVERT: D 1032 TRP cc_start: 0.8476 (m100) cc_final: 0.8099 (m-10) REVERT: D 1035 SER cc_start: 0.8061 (p) cc_final: 0.7695 (t) REVERT: D 1044 VAL cc_start: 0.5323 (OUTLIER) cc_final: 0.5084 (t) REVERT: D 1069 GLU cc_start: 0.6345 (tp30) cc_final: 0.6019 (tm-30) REVERT: D 1077 LYS cc_start: 0.7864 (tttt) cc_final: 0.6571 (ptpp) REVERT: D 1202 ASP cc_start: 0.7320 (t70) cc_final: 0.6967 (t0) outliers start: 81 outliers final: 53 residues processed: 350 average time/residue: 0.1039 time to fit residues: 60.2539 Evaluate side-chains 336 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 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 A residue 1149 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 647 TYR 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 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 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 1021 SER Chi-restraints excluded: chain C residue 1023 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 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 536 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 813 GLU Chi-restraints excluded: chain D residue 1044 VAL 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 1192 VAL 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: 4.9990 chunk 79 optimal weight: 0.0970 chunk 39 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS B 563 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107557 restraints weight = 30494.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110754 restraints weight = 17211.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112661 restraints weight = 12639.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113469 restraints weight = 10752.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114269 restraints weight = 9943.301| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4267 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= 0.115 Angle : 0.534 9.791 26866 Z= 0.278 Chirality : 0.041 0.209 2998 Planarity : 0.003 0.033 3312 Dihedral : 6.683 85.628 2790 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.07 % Allowed : 18.22 % Favored : 78.72 % 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: 0.78 (0.17), residues: 2460 helix: 2.09 (0.14), residues: 1348 sheet: -1.20 (0.43), residues: 142 loop : -1.57 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 715 TYR 0.024 0.001 TYR A1155 PHE 0.014 0.001 PHE D 438 TRP 0.012 0.001 TRP B1063 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00260 (19866) covalent geometry : angle 0.53326 (26842) SS BOND : bond 0.00137 ( 12) SS BOND : angle 1.27508 ( 24) hydrogen bonds : bond 0.03536 ( 1078) hydrogen bonds : angle 3.86899 ( 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 385 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 321 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 642 GLN cc_start: 0.8352 (pp30) cc_final: 0.8041 (pp30) REVERT: B 486 GLU cc_start: 0.7777 (tp30) cc_final: 0.7455 (tp30) REVERT: B 563 GLN cc_start: 0.5870 (mt0) cc_final: 0.4834 (tm-30) REVERT: B 589 CYS cc_start: 0.6719 (t) cc_final: 0.6428 (t) REVERT: B 1005 ARG cc_start: 0.6101 (tmm-80) cc_final: 0.5682 (mtp-110) REVERT: B 1009 MET cc_start: 0.7956 (tpp) cc_final: 0.7701 (tmm) REVERT: B 1032 TRP cc_start: 0.8499 (m100) cc_final: 0.8122 (m-10) REVERT: B 1035 SER cc_start: 0.8161 (p) cc_final: 0.7750 (t) REVERT: B 1077 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6735 (ptpt) REVERT: B 1134 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8721 (tp) REVERT: C 407 MET cc_start: 0.8190 (mtm) cc_final: 0.7975 (mtm) REVERT: C 498 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8929 (pp) REVERT: C 642 GLN cc_start: 0.8418 (pp30) cc_final: 0.8203 (pp30) REVERT: C 1023 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8608 (tpt) REVERT: C 1095 TYR cc_start: 0.7329 (t80) cc_final: 0.6856 (t80) REVERT: D 467 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8382 (mm) REVERT: D 486 GLU cc_start: 0.7682 (tp30) cc_final: 0.7395 (tp30) REVERT: D 656 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8041 (tmtt) REVERT: D 684 ARG cc_start: 0.7847 (pmm150) cc_final: 0.7544 (mtm-85) REVERT: D 705 GLU cc_start: 0.7888 (mp0) cc_final: 0.7636 (mp0) REVERT: D 1032 TRP cc_start: 0.8482 (m100) cc_final: 0.8131 (m-10) REVERT: D 1035 SER cc_start: 0.8134 (p) cc_final: 0.7773 (t) REVERT: D 1044 VAL cc_start: 0.5267 (OUTLIER) cc_final: 0.5054 (t) REVERT: D 1069 GLU cc_start: 0.6324 (tp30) cc_final: 0.6003 (tm-30) REVERT: D 1077 LYS cc_start: 0.7785 (tttt) cc_final: 0.6570 (ptpp) REVERT: D 1202 ASP cc_start: 0.7209 (t70) cc_final: 0.6901 (t0) outliers start: 64 outliers final: 45 residues processed: 360 average time/residue: 0.1109 time to fit residues: 65.2660 Evaluate side-chains 342 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 291 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 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 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 1134 ILE 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 498 LEU 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 1021 SER Chi-restraints excluded: chain C residue 1023 MET 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 813 GLU Chi-restraints excluded: chain D residue 1044 VAL 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: 0.9990 chunk 244 optimal weight: 6.9990 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: 0.9980 chunk 117 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 240 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104787 restraints weight = 31081.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104611 restraints weight = 17900.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105743 restraints weight = 15770.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105965 restraints weight = 13638.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106118 restraints weight = 12740.619| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19878 Z= 0.257 Angle : 0.643 12.529 26866 Z= 0.337 Chirality : 0.045 0.249 2998 Planarity : 0.004 0.035 3312 Dihedral : 6.861 89.646 2790 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.36 % Allowed : 18.46 % Favored : 78.19 % 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: 0.37 (0.17), residues: 2460 helix: 1.72 (0.14), residues: 1334 sheet: -1.30 (0.43), residues: 142 loop : -1.65 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1203 TYR 0.026 0.002 TYR C 523 PHE 0.018 0.002 PHE A1115 TRP 0.010 0.002 TRP C 578 HIS 0.010 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00613 (19866) covalent geometry : angle 0.64159 (26842) SS BOND : bond 0.00285 ( 12) SS BOND : angle 1.45418 ( 24) hydrogen bonds : bond 0.04412 ( 1078) hydrogen bonds : angle 4.25661 ( 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 362 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 292 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: B 563 GLN cc_start: 0.5762 (mt0) cc_final: 0.4753 (tm-30) REVERT: B 647 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: B 1005 ARG cc_start: 0.6370 (tmm-80) cc_final: 0.5850 (mtp-110) REVERT: B 1032 TRP cc_start: 0.8530 (m100) cc_final: 0.8134 (m-10) REVERT: B 1035 SER cc_start: 0.8108 (p) cc_final: 0.7752 (t) REVERT: C 407 MET cc_start: 0.8214 (mtm) cc_final: 0.7825 (mtm) REVERT: C 642 GLN cc_start: 0.8401 (pp30) cc_final: 0.8185 (pp30) REVERT: C 1023 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8404 (tpt) REVERT: C 1095 TYR cc_start: 0.7382 (t80) cc_final: 0.6780 (t80) REVERT: D 467 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8487 (mm) REVERT: D 656 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8058 (tmtt) REVERT: D 684 ARG cc_start: 0.7990 (pmm150) cc_final: 0.7669 (mtm-85) REVERT: D 705 GLU cc_start: 0.7896 (mp0) cc_final: 0.7620 (mp0) REVERT: D 1032 TRP cc_start: 0.8500 (m100) cc_final: 0.8133 (m-10) REVERT: D 1035 SER cc_start: 0.8049 (p) cc_final: 0.7714 (t) REVERT: D 1044 VAL cc_start: 0.5183 (OUTLIER) cc_final: 0.4960 (t) REVERT: D 1069 GLU cc_start: 0.6325 (tp30) cc_final: 0.6055 (tm-30) REVERT: D 1202 ASP cc_start: 0.7340 (t70) cc_final: 0.6943 (t0) outliers start: 70 outliers final: 54 residues processed: 340 average time/residue: 0.1081 time to fit residues: 61.1187 Evaluate side-chains 331 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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 1010 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1135 LEU 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 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 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 1023 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 1184 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 543 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 1044 VAL 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: 0.6980 chunk 36 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 212 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 168 optimal weight: 7.9990 chunk 209 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109389 restraints weight = 30388.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112060 restraints weight = 19680.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112637 restraints weight = 13915.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112686 restraints weight = 11970.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112795 restraints weight = 11363.339| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19878 Z= 0.117 Angle : 0.548 12.836 26866 Z= 0.286 Chirality : 0.041 0.194 2998 Planarity : 0.003 0.033 3312 Dihedral : 6.257 82.423 2790 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.68 % Allowed : 19.18 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.83 (0.17), residues: 2460 helix: 2.18 (0.14), residues: 1336 sheet: -1.29 (0.42), residues: 142 loop : -1.56 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 715 TYR 0.027 0.001 TYR A1155 PHE 0.013 0.001 PHE C 495 TRP 0.012 0.001 TRP B1063 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00264 (19866) covalent geometry : angle 0.54716 (26842) SS BOND : bond 0.00403 ( 12) SS BOND : angle 0.96935 ( 24) hydrogen bonds : bond 0.03533 ( 1078) hydrogen bonds : angle 3.90051 ( 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 369 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 450 TYR cc_start: 0.8173 (m-80) cc_final: 0.7878 (m-80) REVERT: A 1023 MET cc_start: 0.8964 (tpt) cc_final: 0.8713 (tpt) REVERT: B 486 GLU cc_start: 0.7743 (tp30) cc_final: 0.7396 (tp30) REVERT: B 563 GLN cc_start: 0.5759 (mt0) cc_final: 0.4738 (tm-30) REVERT: B 589 CYS cc_start: 0.6720 (t) cc_final: 0.6475 (t) REVERT: B 1005 ARG cc_start: 0.6046 (tmm-80) cc_final: 0.5770 (mtm110) REVERT: B 1032 TRP cc_start: 0.8467 (m100) cc_final: 0.8114 (m-10) REVERT: B 1035 SER cc_start: 0.8252 (p) cc_final: 0.7853 (t) REVERT: C 407 MET cc_start: 0.8120 (mtm) cc_final: 0.7682 (mtm) REVERT: C 642 GLN cc_start: 0.8417 (pp30) cc_final: 0.8214 (pp30) REVERT: C 1063 TRP cc_start: 0.7935 (m-90) cc_final: 0.7731 (m-90) REVERT: C 1095 TYR cc_start: 0.7381 (t80) cc_final: 0.6883 (t80) REVERT: D 467 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8447 (mm) REVERT: D 486 GLU cc_start: 0.7707 (tp30) cc_final: 0.7389 (tp30) REVERT: D 656 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8051 (tmtt) REVERT: D 684 ARG cc_start: 0.7896 (pmm150) cc_final: 0.7597 (mtm-85) REVERT: D 1032 TRP cc_start: 0.8463 (m100) cc_final: 0.8123 (m-10) REVERT: D 1035 SER cc_start: 0.8201 (p) cc_final: 0.7838 (t) REVERT: D 1069 GLU cc_start: 0.6257 (tp30) cc_final: 0.6052 (tm-30) REVERT: D 1202 ASP cc_start: 0.7236 (t70) cc_final: 0.6878 (t0) outliers start: 56 outliers final: 49 residues processed: 349 average time/residue: 0.1137 time to fit residues: 65.4158 Evaluate side-chains 345 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 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 A residue 1135 LEU Chi-restraints excluded: chain B residue 407 MET 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 1044 VAL 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 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 1021 SER Chi-restraints excluded: chain C residue 1023 MET 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 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 746 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 813 GLU 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: 0.0670 chunk 9 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110595 restraints weight = 30584.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111493 restraints weight = 16599.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111733 restraints weight = 13716.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111831 restraints weight = 13317.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113297 restraints weight = 12413.321| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19878 Z= 0.116 Angle : 0.558 12.843 26866 Z= 0.289 Chirality : 0.041 0.197 2998 Planarity : 0.003 0.032 3312 Dihedral : 5.928 78.258 2790 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.40 % Allowed : 20.04 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.91 (0.17), residues: 2460 helix: 2.29 (0.14), residues: 1336 sheet: -1.50 (0.38), residues: 166 loop : -1.53 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1036 TYR 0.036 0.001 TYR C 732 PHE 0.022 0.001 PHE B 438 TRP 0.011 0.001 TRP B1063 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00264 (19866) covalent geometry : angle 0.55761 (26842) SS BOND : bond 0.00173 ( 12) SS BOND : angle 1.01599 ( 24) hydrogen bonds : bond 0.03449 ( 1078) hydrogen bonds : angle 3.81769 ( 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 356 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 306 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 431 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 450 TYR cc_start: 0.8208 (m-80) cc_final: 0.7827 (m-80) REVERT: A 1023 MET cc_start: 0.8943 (tpt) cc_final: 0.8723 (tpt) REVERT: B 486 GLU cc_start: 0.7740 (tp30) cc_final: 0.7415 (tp30) REVERT: B 563 GLN cc_start: 0.5680 (mt0) cc_final: 0.4715 (tm-30) REVERT: B 1005 ARG cc_start: 0.5962 (tmm-80) cc_final: 0.5612 (mtp-110) REVERT: B 1032 TRP cc_start: 0.8491 (m100) cc_final: 0.8125 (m-10) REVERT: B 1035 SER cc_start: 0.8156 (p) cc_final: 0.7745 (t) REVERT: C 407 MET cc_start: 0.8146 (mtm) cc_final: 0.7699 (mtm) REVERT: C 642 GLN cc_start: 0.8448 (pp30) cc_final: 0.8235 (pp30) REVERT: C 1095 TYR cc_start: 0.7364 (t80) cc_final: 0.6885 (t80) REVERT: D 467 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8447 (mm) REVERT: D 486 GLU cc_start: 0.7688 (tp30) cc_final: 0.7386 (tp30) REVERT: D 656 LYS cc_start: 0.8390 (ttmt) cc_final: 0.8045 (tmtt) REVERT: D 684 ARG cc_start: 0.7945 (pmm150) cc_final: 0.7627 (mtm-85) REVERT: D 1032 TRP cc_start: 0.8470 (m100) cc_final: 0.8119 (m-10) REVERT: D 1035 SER cc_start: 0.8184 (p) cc_final: 0.7811 (t) REVERT: D 1069 GLU cc_start: 0.6268 (tp30) cc_final: 0.6034 (tm-30) REVERT: D 1202 ASP cc_start: 0.7262 (t70) cc_final: 0.6882 (t0) outliers start: 50 outliers final: 46 residues processed: 338 average time/residue: 0.1067 time to fit residues: 59.2144 Evaluate side-chains 343 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 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 407 MET 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 1044 VAL 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 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 1010 LEU Chi-restraints excluded: chain C residue 1023 MET 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 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 746 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 813 GLU 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: 2.9990 chunk 194 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS B 791 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110958 restraints weight = 30606.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111291 restraints weight = 19389.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112213 restraints weight = 15653.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112454 restraints weight = 13404.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112542 restraints weight = 12497.705| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19878 Z= 0.117 Angle : 0.559 12.822 26866 Z= 0.288 Chirality : 0.041 0.194 2998 Planarity : 0.003 0.032 3312 Dihedral : 5.595 73.447 2790 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.25 % Allowed : 20.57 % Favored : 77.18 % 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: 0.96 (0.17), residues: 2460 helix: 2.32 (0.14), residues: 1338 sheet: -1.45 (0.39), residues: 166 loop : -1.52 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 715 TYR 0.026 0.001 TYR A1155 PHE 0.020 0.001 PHE B1126 TRP 0.010 0.001 TRP B1063 HIS 0.012 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00269 (19866) covalent geometry : angle 0.55839 (26842) SS BOND : bond 0.00226 ( 12) SS BOND : angle 0.90919 ( 24) hydrogen bonds : bond 0.03429 ( 1078) hydrogen bonds : angle 3.80443 ( 3138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2797.03 seconds wall clock time: 50 minutes 10.71 seconds (3010.71 seconds total)