Starting phenix.real_space_refine on Sat Sep 28 14:21:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/09_2024/7tnl_26013.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/09_2024/7tnl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/09_2024/7tnl_26013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/09_2024/7tnl_26013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/09_2024/7tnl_26013.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnl_26013/09_2024/7tnl_26013.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12558 2.51 5 N 3144 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19434 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4828 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4828 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.97, per 1000 atoms: 0.56 Number of scatterers: 19434 At special positions: 0 Unit cell: (123.67, 115.37, 131.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3592 8.00 N 3144 7.00 C 12558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.04 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.01 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.04 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.04 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.01 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 2.1 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 22 sheets defined 55.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 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: 5.82 Time building geometry restraints manager: 4.76 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1209 \ or resid 1302)) selection = (chain 'B' and (resid 394 through 549 or resid 564 through 1209 or resid 1301)) selection = (chain 'C' and (resid 394 through 548 or (resid 549 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 819 or resid 1002 through 1209 \ or resid 1302)) selection = (chain 'D' and (resid 394 through 549 or resid 564 through 1209 or resid 1301)) } 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.140 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.680 ------------------------------------------------------------------------------- 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 19866 Z= 0.595 Angle : 1.029 11.924 26842 Z= 0.555 Chirality : 0.059 0.356 2998 Planarity : 0.007 0.057 3312 Dihedral : 11.859 120.568 7212 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.63 % Favored : 95.12 % Rotamer: Outliers : 0.38 % Allowed : 5.75 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.12), residues: 2460 helix: -3.43 (0.07), residues: 1320 sheet: -1.45 (0.35), residues: 168 loop : -2.12 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP A 671 HIS 0.007 0.003 HIS A1131 PHE 0.038 0.003 PHE C 623 TYR 0.028 0.003 TYR D 702 ARG 0.012 0.001 ARG A 599 *********************** 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 fitting. rotamer outliers: 8 poor density : 554 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7602 (mpt) cc_final: 0.7376 (mtp) REVERT: A 668 ASP cc_start: 0.7611 (t70) cc_final: 0.7335 (t0) REVERT: A 695 LYS cc_start: 0.8648 (mptt) cc_final: 0.8349 (pttp) REVERT: A 817 LYS cc_start: 0.7706 (mmtp) cc_final: 0.7440 (mtmt) REVERT: A 1095 TYR cc_start: 0.7152 (t80) cc_final: 0.6949 (t80) REVERT: A 1126 PHE cc_start: 0.7627 (t80) cc_final: 0.7358 (m-80) REVERT: B 399 THR cc_start: 0.9289 (t) cc_final: 0.8967 (m) REVERT: B 410 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7875 (mmmm) REVERT: B 412 HIS cc_start: 0.6831 (p90) cc_final: 0.6592 (p90) REVERT: B 642 GLN cc_start: 0.8006 (pp30) cc_final: 0.7698 (pp30) REVERT: B 656 LYS cc_start: 0.8729 (tttt) cc_final: 0.8277 (ttmt) REVERT: B 684 ARG cc_start: 0.7990 (pmm150) cc_final: 0.7541 (mtm-85) REVERT: B 713 GLU cc_start: 0.7577 (tt0) cc_final: 0.7302 (tt0) REVERT: B 1035 SER cc_start: 0.8127 (p) cc_final: 0.7787 (t) REVERT: B 1119 LEU cc_start: 0.7361 (tt) cc_final: 0.6972 (tp) REVERT: B 1200 PHE cc_start: 0.8409 (t80) cc_final: 0.8134 (t80) REVERT: B 1202 ASP cc_start: 0.7815 (t70) cc_final: 0.7576 (t0) REVERT: C 414 MET cc_start: 0.7602 (mpt) cc_final: 0.7342 (mtp) REVERT: C 668 ASP cc_start: 0.7648 (t70) cc_final: 0.7362 (t0) REVERT: C 695 LYS cc_start: 0.8606 (mptt) cc_final: 0.8371 (pttp) REVERT: C 788 SER cc_start: 0.8751 (m) cc_final: 0.8469 (t) REVERT: C 813 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6730 (tp30) REVERT: C 1095 TYR cc_start: 0.7250 (t80) cc_final: 0.7044 (t80) REVERT: C 1114 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8659 (mm) REVERT: C 1173 TYR cc_start: 0.7832 (p90) cc_final: 0.7567 (p90) REVERT: D 410 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7771 (mmmm) REVERT: D 467 LEU cc_start: 0.8577 (mt) cc_final: 0.8367 (mt) REVERT: D 642 GLN cc_start: 0.7949 (pp30) cc_final: 0.7584 (pp30) REVERT: D 656 LYS cc_start: 0.8528 (tttt) cc_final: 0.8185 (ttmt) REVERT: D 684 ARG cc_start: 0.7915 (pmm150) cc_final: 0.7549 (mtm-85) REVERT: D 713 GLU cc_start: 0.7503 (tt0) cc_final: 0.7270 (tt0) REVERT: D 813 GLU cc_start: 0.7558 (pp20) cc_final: 0.7263 (tm-30) REVERT: D 1035 SER cc_start: 0.8152 (p) cc_final: 0.7792 (t) REVERT: D 1108 ILE cc_start: 0.8873 (mt) cc_final: 0.8616 (pt) REVERT: D 1115 PHE cc_start: 0.7943 (t80) cc_final: 0.7708 (t80) REVERT: D 1202 ASP cc_start: 0.7265 (t70) cc_final: 0.6778 (t0) outliers start: 8 outliers final: 0 residues processed: 560 average time/residue: 0.3115 time to fit residues: 258.4849 Evaluate side-chains 306 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1114 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 chunk 225 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 714 GLN A 756 GLN A1206 GLN B 791 ASN B1071 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS C 756 GLN C1131 HIS C1206 GLN D 791 ASN D1071 ASN ** D1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19866 Z= 0.187 Angle : 0.591 9.387 26842 Z= 0.313 Chirality : 0.041 0.213 2998 Planarity : 0.004 0.043 3312 Dihedral : 8.680 103.828 2790 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.49 % Allowed : 11.94 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 2460 helix: -0.04 (0.12), residues: 1330 sheet: -1.27 (0.39), residues: 142 loop : -1.79 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 766 HIS 0.017 0.002 HIS A1059 PHE 0.021 0.001 PHE D1200 TYR 0.022 0.001 TYR C 523 ARG 0.005 0.001 ARG D1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 399 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7642 (mpt) cc_final: 0.7377 (mtp) REVERT: A 695 LYS cc_start: 0.8523 (mptt) cc_final: 0.8221 (pttp) REVERT: A 795 VAL cc_start: 0.9255 (t) cc_final: 0.9054 (p) REVERT: A 1025 ILE cc_start: 0.8404 (mm) cc_final: 0.8176 (mm) REVERT: A 1126 PHE cc_start: 0.7587 (t80) cc_final: 0.7283 (m-80) REVERT: B 410 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7811 (mmmm) REVERT: B 563 GLN cc_start: 0.5195 (mt0) cc_final: 0.4618 (tm-30) REVERT: B 642 GLN cc_start: 0.8155 (pp30) cc_final: 0.7796 (pp30) REVERT: B 656 LYS cc_start: 0.8522 (tttt) cc_final: 0.8133 (tmtt) REVERT: B 684 ARG cc_start: 0.8086 (pmm150) cc_final: 0.7816 (mtm-85) REVERT: B 713 GLU cc_start: 0.7524 (tt0) cc_final: 0.7293 (tt0) REVERT: B 1009 MET cc_start: 0.8121 (tpp) cc_final: 0.7668 (tmm) REVERT: B 1032 TRP cc_start: 0.8511 (m100) cc_final: 0.8133 (m-10) REVERT: B 1035 SER cc_start: 0.8130 (p) cc_final: 0.7746 (t) REVERT: B 1199 MET cc_start: 0.7971 (mmm) cc_final: 0.7689 (mmt) REVERT: B 1200 PHE cc_start: 0.8368 (t80) cc_final: 0.8098 (t80) REVERT: C 414 MET cc_start: 0.7774 (mpt) cc_final: 0.7530 (mtp) REVERT: C 642 GLN cc_start: 0.8273 (pp30) cc_final: 0.7917 (pp30) REVERT: C 695 LYS cc_start: 0.8519 (mptt) cc_final: 0.8311 (pttp) REVERT: C 742 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7500 (pp) REVERT: C 813 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6643 (tp30) REVERT: C 1095 TYR cc_start: 0.7258 (t80) cc_final: 0.6679 (t80) REVERT: C 1150 ILE cc_start: 0.8955 (tp) cc_final: 0.8735 (tp) REVERT: D 684 ARG cc_start: 0.7944 (pmm150) cc_final: 0.7608 (mtm-85) REVERT: D 713 GLU cc_start: 0.7433 (tt0) cc_final: 0.7229 (tt0) REVERT: D 1035 SER cc_start: 0.8106 (p) cc_final: 0.7714 (t) REVERT: D 1125 GLU cc_start: 0.7415 (tp30) cc_final: 0.7163 (tm-30) REVERT: D 1202 ASP cc_start: 0.7190 (t70) cc_final: 0.6842 (t0) outliers start: 52 outliers final: 18 residues processed: 437 average time/residue: 0.2600 time to fit residues: 177.3202 Evaluate side-chains 330 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 311 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1191 MET Chi-restraints excluded: chain D residue 1172 SER Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19866 Z= 0.232 Angle : 0.569 8.530 26842 Z= 0.299 Chirality : 0.041 0.188 2998 Planarity : 0.004 0.037 3312 Dihedral : 8.171 96.642 2790 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.31 % Allowed : 14.19 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2460 helix: 1.34 (0.14), residues: 1330 sheet: -1.30 (0.39), residues: 152 loop : -1.62 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1063 HIS 0.015 0.002 HIS A1059 PHE 0.013 0.002 PHE A 495 TYR 0.021 0.001 TYR C 523 ARG 0.004 0.000 ARG D1036 *********************** 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 392 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 323 time to evaluate : 3.315 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7754 (mpt) cc_final: 0.7546 (mtp) REVERT: A 642 GLN cc_start: 0.8459 (pp30) cc_final: 0.8075 (pp30) REVERT: A 695 LYS cc_start: 0.8548 (mptt) cc_final: 0.8123 (pttp) REVERT: A 795 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9041 (p) REVERT: A 1025 ILE cc_start: 0.8411 (mm) cc_final: 0.8207 (mm) REVERT: A 1126 PHE cc_start: 0.7497 (t80) cc_final: 0.7216 (m-80) REVERT: B 563 GLN cc_start: 0.5173 (mt0) cc_final: 0.4632 (tm-30) REVERT: B 642 GLN cc_start: 0.8224 (pp30) cc_final: 0.7856 (pp30) REVERT: B 656 LYS cc_start: 0.8546 (tttt) cc_final: 0.8188 (tmtt) REVERT: B 684 ARG cc_start: 0.8080 (pmm150) cc_final: 0.7819 (mtm-85) REVERT: B 713 GLU cc_start: 0.7545 (tt0) cc_final: 0.7316 (tt0) REVERT: B 1005 ARG cc_start: 0.6673 (tmm-80) cc_final: 0.5996 (mtm110) REVERT: B 1009 MET cc_start: 0.8158 (tpp) cc_final: 0.7735 (tmm) REVERT: B 1032 TRP cc_start: 0.8513 (m100) cc_final: 0.8155 (m-10) REVERT: B 1035 SER cc_start: 0.8138 (p) cc_final: 0.7718 (t) REVERT: B 1113 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8424 (mt) REVERT: B 1199 MET cc_start: 0.7953 (mmm) cc_final: 0.7746 (mmt) REVERT: C 414 MET cc_start: 0.7826 (mpt) cc_final: 0.7567 (mtp) REVERT: C 695 LYS cc_start: 0.8569 (mptt) cc_final: 0.8368 (pttp) REVERT: C 742 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7537 (pp) REVERT: C 813 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6645 (tp30) REVERT: C 1095 TYR cc_start: 0.7256 (t80) cc_final: 0.6696 (t80) REVERT: C 1198 HIS cc_start: 0.8135 (m-70) cc_final: 0.7867 (m-70) REVERT: D 486 GLU cc_start: 0.7623 (tp30) cc_final: 0.7261 (tp30) REVERT: D 684 ARG cc_start: 0.8002 (pmm150) cc_final: 0.7686 (mtm-85) REVERT: D 713 GLU cc_start: 0.7476 (tt0) cc_final: 0.7265 (tt0) REVERT: D 1035 SER cc_start: 0.8114 (p) cc_final: 0.7697 (t) REVERT: D 1202 ASP cc_start: 0.7298 (t70) cc_final: 0.6980 (t0) outliers start: 69 outliers final: 41 residues processed: 369 average time/residue: 0.2837 time to fit residues: 167.5277 Evaluate side-chains 333 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 289 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1027 VAL 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 746 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19866 Z= 0.393 Angle : 0.643 9.353 26842 Z= 0.339 Chirality : 0.045 0.217 2998 Planarity : 0.004 0.038 3312 Dihedral : 8.215 94.954 2790 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.93 % Allowed : 14.77 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2460 helix: 1.41 (0.14), residues: 1330 sheet: -1.03 (0.43), residues: 142 loop : -1.67 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1063 HIS 0.012 0.002 HIS A1059 PHE 0.018 0.002 PHE B1200 TYR 0.025 0.002 TYR C 523 ARG 0.004 0.001 ARG D1036 *********************** 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 389 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 307 time to evaluate : 2.302 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7858 (mpt) cc_final: 0.7583 (mtp) REVERT: A 695 LYS cc_start: 0.8586 (mptt) cc_final: 0.8230 (pttp) REVERT: A 795 VAL cc_start: 0.9299 (OUTLIER) cc_final: 0.9051 (p) REVERT: A 817 LYS cc_start: 0.7416 (mmtp) cc_final: 0.7197 (mttt) REVERT: A 1025 ILE cc_start: 0.8454 (mm) cc_final: 0.8242 (mm) REVERT: A 1126 PHE cc_start: 0.7445 (t80) cc_final: 0.7161 (m-80) REVERT: A 1204 HIS cc_start: 0.7185 (t-90) cc_final: 0.6817 (t-90) REVERT: B 642 GLN cc_start: 0.8162 (pp30) cc_final: 0.7881 (pp30) REVERT: B 647 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: B 656 LYS cc_start: 0.8595 (tttt) cc_final: 0.8233 (tmtt) REVERT: B 684 ARG cc_start: 0.8106 (pmm150) cc_final: 0.7846 (mtm-85) REVERT: B 713 GLU cc_start: 0.7576 (tt0) cc_final: 0.7361 (tt0) REVERT: B 1009 MET cc_start: 0.8135 (tpp) cc_final: 0.7865 (tmm) REVERT: B 1032 TRP cc_start: 0.8546 (m100) cc_final: 0.8189 (m-10) REVERT: B 1035 SER cc_start: 0.8018 (p) cc_final: 0.7649 (t) REVERT: B 1125 GLU cc_start: 0.7888 (tp30) cc_final: 0.7429 (tm-30) REVERT: C 414 MET cc_start: 0.7837 (mpt) cc_final: 0.7581 (mtp) REVERT: C 695 LYS cc_start: 0.8560 (mptt) cc_final: 0.8180 (pttp) REVERT: C 742 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7661 (pp) REVERT: C 813 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6612 (tp30) REVERT: C 1095 TYR cc_start: 0.7372 (t80) cc_final: 0.6776 (t80) REVERT: C 1198 HIS cc_start: 0.8273 (m-70) cc_final: 0.8071 (m-70) REVERT: D 467 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8457 (mm) REVERT: D 486 GLU cc_start: 0.7944 (tp30) cc_final: 0.7592 (tp30) REVERT: D 684 ARG cc_start: 0.8020 (pmm150) cc_final: 0.7666 (mtm-85) REVERT: D 705 GLU cc_start: 0.7934 (mp0) cc_final: 0.7670 (mp0) REVERT: D 713 GLU cc_start: 0.7546 (tt0) cc_final: 0.7331 (tt0) REVERT: D 813 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7535 (pt0) REVERT: D 1032 TRP cc_start: 0.8497 (m100) cc_final: 0.8137 (m-10) REVERT: D 1035 SER cc_start: 0.7981 (p) cc_final: 0.7606 (t) REVERT: D 1069 GLU cc_start: 0.6541 (tp30) cc_final: 0.6131 (tm-30) REVERT: D 1077 LYS cc_start: 0.7802 (pttt) cc_final: 0.6498 (ptpp) REVERT: D 1202 ASP cc_start: 0.7272 (t70) cc_final: 0.7033 (t0) outliers start: 82 outliers final: 43 residues processed: 360 average time/residue: 0.2667 time to fit residues: 156.1115 Evaluate side-chains 334 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 287 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 1010 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 647 TYR Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1134 ILE Chi-restraints excluded: chain B residue 1187 ILE Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 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 693 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1057 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 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 Chi-restraints excluded: chain D residue 1192 VAL Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.6980 chunk 136 optimal weight: 0.0060 chunk 3 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 98 optimal weight: 0.0370 chunk 204 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9478 ------------------------------------------------------------------------------- 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** C 756 GLN C1131 HIS ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19866 Z= 0.190 Angle : 0.544 7.077 26842 Z= 0.286 Chirality : 0.041 0.177 2998 Planarity : 0.003 0.035 3312 Dihedral : 7.652 89.194 2790 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.31 % Allowed : 15.77 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2460 helix: 1.86 (0.14), residues: 1344 sheet: -1.07 (0.43), residues: 142 loop : -1.65 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 766 HIS 0.011 0.001 HIS A1059 PHE 0.016 0.001 PHE D 438 TYR 0.024 0.001 TYR A1155 ARG 0.003 0.000 ARG B1005 *********************** 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 389 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 320 time to evaluate : 2.081 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8087 (mtm) cc_final: 0.7788 (mtt) REVERT: A 414 MET cc_start: 0.7859 (mpt) cc_final: 0.7583 (mtp) REVERT: A 642 GLN cc_start: 0.8376 (pp30) cc_final: 0.8093 (pp30) REVERT: A 695 LYS cc_start: 0.8515 (mptt) cc_final: 0.8184 (pttp) REVERT: A 795 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.9045 (p) REVERT: A 1126 PHE cc_start: 0.7421 (t80) cc_final: 0.7135 (m-80) REVERT: B 563 GLN cc_start: 0.5589 (mt0) cc_final: 0.4616 (tm-30) REVERT: B 589 CYS cc_start: 0.6822 (t) cc_final: 0.6545 (t) REVERT: B 642 GLN cc_start: 0.8154 (pp30) cc_final: 0.7932 (pp30) REVERT: B 656 LYS cc_start: 0.8570 (tttt) cc_final: 0.8248 (tmtt) REVERT: B 684 ARG cc_start: 0.8031 (pmm150) cc_final: 0.7758 (mtm-85) REVERT: B 713 GLU cc_start: 0.7491 (tt0) cc_final: 0.7236 (tt0) REVERT: B 1005 ARG cc_start: 0.6591 (tmm-80) cc_final: 0.5457 (mtm110) REVERT: B 1032 TRP cc_start: 0.8525 (m100) cc_final: 0.8142 (m-10) REVERT: B 1035 SER cc_start: 0.8071 (p) cc_final: 0.7679 (t) REVERT: B 1077 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6494 (ptpp) REVERT: B 1125 GLU cc_start: 0.7762 (tp30) cc_final: 0.7536 (tm-30) REVERT: C 414 MET cc_start: 0.7875 (mpt) cc_final: 0.7602 (mtp) REVERT: C 642 GLN cc_start: 0.8292 (pp30) cc_final: 0.7988 (pp30) REVERT: C 695 LYS cc_start: 0.8568 (mptt) cc_final: 0.8197 (pttp) REVERT: C 742 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7759 (pp) REVERT: C 1095 TYR cc_start: 0.7334 (t80) cc_final: 0.6777 (t80) REVERT: C 1148 ASN cc_start: 0.8482 (t0) cc_final: 0.8141 (t0) REVERT: C 1150 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8775 (tp) REVERT: D 467 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8463 (mm) REVERT: D 486 GLU cc_start: 0.7818 (tp30) cc_final: 0.7423 (tp30) REVERT: D 563 GLN cc_start: 0.5333 (mt0) cc_final: 0.4572 (tm-30) REVERT: D 684 ARG cc_start: 0.8013 (pmm150) cc_final: 0.7681 (mtm-85) REVERT: D 705 GLU cc_start: 0.7897 (mp0) cc_final: 0.7665 (mp0) REVERT: D 713 GLU cc_start: 0.7465 (tt0) cc_final: 0.7200 (tt0) REVERT: D 813 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7583 (pt0) REVERT: D 1032 TRP cc_start: 0.8486 (m100) cc_final: 0.8140 (m-10) REVERT: D 1035 SER cc_start: 0.7979 (p) cc_final: 0.7613 (t) REVERT: D 1077 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.6420 (ptpp) REVERT: D 1202 ASP cc_start: 0.7284 (t70) cc_final: 0.6964 (t0) outliers start: 69 outliers final: 37 residues processed: 363 average time/residue: 0.2645 time to fit residues: 153.5497 Evaluate side-chains 331 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 288 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU 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 1192 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 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 1150 ILE Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1008 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19866 Z= 0.211 Angle : 0.543 7.149 26842 Z= 0.285 Chirality : 0.041 0.186 2998 Planarity : 0.003 0.034 3312 Dihedral : 7.234 87.340 2790 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.07 % Allowed : 16.35 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2460 helix: 1.98 (0.14), residues: 1346 sheet: -1.41 (0.41), residues: 152 loop : -1.58 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 766 HIS 0.009 0.001 HIS A1059 PHE 0.014 0.001 PHE D 438 TYR 0.028 0.001 TYR A1155 ARG 0.007 0.000 ARG D1005 *********************** 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 373 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 309 time to evaluate : 2.010 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7874 (mpt) cc_final: 0.7596 (mtp) REVERT: A 695 LYS cc_start: 0.8544 (mptt) cc_final: 0.8141 (pttp) REVERT: A 795 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9041 (p) REVERT: A 1126 PHE cc_start: 0.7416 (t80) cc_final: 0.7120 (m-80) REVERT: B 563 GLN cc_start: 0.5576 (mt0) cc_final: 0.4573 (tm-30) REVERT: B 589 CYS cc_start: 0.6850 (t) cc_final: 0.6612 (t) REVERT: B 656 LYS cc_start: 0.8592 (tttt) cc_final: 0.8334 (tmtt) REVERT: B 684 ARG cc_start: 0.8034 (pmm150) cc_final: 0.7758 (mtm-85) REVERT: B 705 GLU cc_start: 0.7864 (mp0) cc_final: 0.7647 (mp0) REVERT: B 713 GLU cc_start: 0.7529 (tt0) cc_final: 0.7246 (tt0) REVERT: B 1005 ARG cc_start: 0.5935 (tmm-80) cc_final: 0.5294 (mtm110) REVERT: B 1032 TRP cc_start: 0.8548 (m100) cc_final: 0.8173 (m-10) REVERT: B 1035 SER cc_start: 0.8039 (p) cc_final: 0.7630 (t) REVERT: B 1069 GLU cc_start: 0.6408 (tp30) cc_final: 0.6157 (tm-30) REVERT: B 1125 GLU cc_start: 0.7704 (tp30) cc_final: 0.7461 (pt0) REVERT: C 414 MET cc_start: 0.7880 (mpt) cc_final: 0.7600 (mtp) REVERT: C 695 LYS cc_start: 0.8575 (mptt) cc_final: 0.8185 (pttp) REVERT: C 742 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7745 (pp) REVERT: C 1095 TYR cc_start: 0.7349 (t80) cc_final: 0.6838 (t80) REVERT: C 1150 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8767 (tp) REVERT: D 467 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8479 (mm) REVERT: D 486 GLU cc_start: 0.7868 (tp30) cc_final: 0.7452 (tp30) REVERT: D 563 GLN cc_start: 0.5415 (mt0) cc_final: 0.4641 (tm-30) REVERT: D 684 ARG cc_start: 0.8025 (pmm150) cc_final: 0.7704 (mtm-85) REVERT: D 705 GLU cc_start: 0.7927 (mp0) cc_final: 0.7682 (mp0) REVERT: D 713 GLU cc_start: 0.7488 (tt0) cc_final: 0.7212 (tt0) REVERT: D 813 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7566 (pt0) REVERT: D 1032 TRP cc_start: 0.8502 (m100) cc_final: 0.8133 (m-10) REVERT: D 1035 SER cc_start: 0.7976 (p) cc_final: 0.7606 (t) REVERT: D 1069 GLU cc_start: 0.6507 (tp30) cc_final: 0.5961 (tm-30) REVERT: D 1077 LYS cc_start: 0.7730 (pttt) cc_final: 0.6444 (ptpp) REVERT: D 1202 ASP cc_start: 0.7326 (t70) cc_final: 0.7062 (t0) outliers start: 64 outliers final: 46 residues processed: 346 average time/residue: 0.2579 time to fit residues: 144.6393 Evaluate side-chains 341 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 291 time to evaluate : 2.077 ------------------------------------------------------------------------------- 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 1114 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1150 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 503 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 239 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 B1131 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19866 Z= 0.220 Angle : 0.547 7.147 26842 Z= 0.287 Chirality : 0.041 0.226 2998 Planarity : 0.003 0.034 3312 Dihedral : 6.746 84.559 2790 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.16 % Allowed : 17.69 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2460 helix: 2.02 (0.14), residues: 1346 sheet: -1.43 (0.41), residues: 152 loop : -1.57 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 766 HIS 0.009 0.001 HIS A1059 PHE 0.013 0.001 PHE D 438 TYR 0.024 0.001 TYR A1155 ARG 0.004 0.000 ARG D1005 *********************** 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 367 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 301 time to evaluate : 2.204 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7879 (mpt) cc_final: 0.7599 (mtp) REVERT: A 498 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8877 (pp) REVERT: A 642 GLN cc_start: 0.8288 (pp30) cc_final: 0.8014 (pp30) REVERT: A 695 LYS cc_start: 0.8519 (mptt) cc_final: 0.8157 (pttp) REVERT: A 795 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9049 (p) REVERT: A 1126 PHE cc_start: 0.7372 (t80) cc_final: 0.7074 (m-80) REVERT: B 486 GLU cc_start: 0.7923 (tp30) cc_final: 0.7578 (tp30) REVERT: B 563 GLN cc_start: 0.5593 (mt0) cc_final: 0.4614 (tm-30) REVERT: B 589 CYS cc_start: 0.6878 (t) cc_final: 0.6650 (t) REVERT: B 656 LYS cc_start: 0.8598 (tttt) cc_final: 0.8331 (tmtt) REVERT: B 684 ARG cc_start: 0.8049 (pmm150) cc_final: 0.7762 (mtm-85) REVERT: B 705 GLU cc_start: 0.7944 (mp0) cc_final: 0.7693 (mp0) REVERT: B 713 GLU cc_start: 0.7547 (tt0) cc_final: 0.7242 (tt0) REVERT: B 1005 ARG cc_start: 0.5967 (tmm-80) cc_final: 0.5403 (mtm110) REVERT: B 1032 TRP cc_start: 0.8549 (m100) cc_final: 0.8169 (m-10) REVERT: B 1035 SER cc_start: 0.8081 (p) cc_final: 0.7684 (t) REVERT: B 1069 GLU cc_start: 0.6499 (tp30) cc_final: 0.6101 (tm-30) REVERT: B 1125 GLU cc_start: 0.7726 (tp30) cc_final: 0.7499 (pt0) REVERT: C 414 MET cc_start: 0.7899 (mpt) cc_final: 0.7589 (mtp) REVERT: C 642 GLN cc_start: 0.8261 (pp30) cc_final: 0.7973 (pp30) REVERT: C 695 LYS cc_start: 0.8535 (mptt) cc_final: 0.8114 (pttp) REVERT: C 742 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7711 (pp) REVERT: C 1063 TRP cc_start: 0.7936 (m-90) cc_final: 0.7708 (m-90) REVERT: C 1095 TYR cc_start: 0.7354 (t80) cc_final: 0.6841 (t80) REVERT: C 1150 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8779 (tp) REVERT: D 467 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8489 (mm) REVERT: D 486 GLU cc_start: 0.7878 (tp30) cc_final: 0.7461 (tp30) REVERT: D 563 GLN cc_start: 0.5559 (mt0) cc_final: 0.4759 (tm-30) REVERT: D 656 LYS cc_start: 0.8455 (ttmt) cc_final: 0.7954 (tmtt) REVERT: D 684 ARG cc_start: 0.8025 (pmm150) cc_final: 0.7714 (mtm-85) REVERT: D 705 GLU cc_start: 0.7921 (mp0) cc_final: 0.7671 (mp0) REVERT: D 713 GLU cc_start: 0.7503 (tt0) cc_final: 0.7214 (tt0) REVERT: D 813 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7561 (pt0) REVERT: D 1032 TRP cc_start: 0.8509 (m100) cc_final: 0.8141 (m-10) REVERT: D 1035 SER cc_start: 0.7990 (p) cc_final: 0.7631 (t) REVERT: D 1044 VAL cc_start: 0.5332 (OUTLIER) cc_final: 0.5130 (t) REVERT: D 1077 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.6407 (ptpp) REVERT: D 1202 ASP cc_start: 0.7339 (t70) cc_final: 0.7059 (t0) outliers start: 66 outliers final: 49 residues processed: 340 average time/residue: 0.2611 time to fit residues: 142.9348 Evaluate side-chains 337 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 281 time to evaluate : 2.081 ------------------------------------------------------------------------------- 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 498 LEU 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 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1116 MET Chi-restraints excluded: chain B residue 1192 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 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1150 ILE Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 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 536 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19866 Z= 0.203 Angle : 0.534 7.104 26842 Z= 0.281 Chirality : 0.041 0.216 2998 Planarity : 0.003 0.033 3312 Dihedral : 6.260 81.415 2790 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.97 % Allowed : 18.22 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2460 helix: 2.12 (0.14), residues: 1338 sheet: -1.18 (0.43), residues: 142 loop : -1.56 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1063 HIS 0.009 0.001 HIS B 412 PHE 0.014 0.001 PHE D 438 TYR 0.023 0.001 TYR A1155 ARG 0.004 0.000 ARG D1005 *********************** 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 360 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 298 time to evaluate : 1.969 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7937 (mpt) cc_final: 0.7663 (mtp) REVERT: A 498 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8842 (pp) REVERT: A 642 GLN cc_start: 0.8291 (pp30) cc_final: 0.7992 (pp30) REVERT: A 695 LYS cc_start: 0.8464 (mptt) cc_final: 0.8135 (pttp) REVERT: A 732 TYR cc_start: 0.8959 (m-10) cc_final: 0.8753 (m-10) REVERT: A 795 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.9053 (p) REVERT: A 1023 MET cc_start: 0.9006 (tpt) cc_final: 0.8774 (tpt) REVERT: A 1126 PHE cc_start: 0.7381 (t80) cc_final: 0.7124 (m-80) REVERT: B 486 GLU cc_start: 0.7889 (tp30) cc_final: 0.7537 (tp30) REVERT: B 563 GLN cc_start: 0.5598 (mt0) cc_final: 0.4644 (tm-30) REVERT: B 589 CYS cc_start: 0.6837 (t) cc_final: 0.6578 (t) REVERT: B 656 LYS cc_start: 0.8594 (tttt) cc_final: 0.8339 (tmtt) REVERT: B 684 ARG cc_start: 0.8039 (pmm150) cc_final: 0.7759 (mtm-85) REVERT: B 705 GLU cc_start: 0.7943 (mp0) cc_final: 0.7687 (mp0) REVERT: B 713 GLU cc_start: 0.7529 (tt0) cc_final: 0.7253 (tt0) REVERT: B 1005 ARG cc_start: 0.5854 (tmm-80) cc_final: 0.5334 (mtm110) REVERT: B 1032 TRP cc_start: 0.8548 (m100) cc_final: 0.8163 (m-10) REVERT: B 1035 SER cc_start: 0.8074 (p) cc_final: 0.7665 (t) REVERT: B 1069 GLU cc_start: 0.6444 (tp30) cc_final: 0.6116 (tm-30) REVERT: B 1125 GLU cc_start: 0.7757 (tp30) cc_final: 0.7427 (pt0) REVERT: C 414 MET cc_start: 0.7940 (mpt) cc_final: 0.7631 (mtp) REVERT: C 642 GLN cc_start: 0.8244 (pp30) cc_final: 0.7928 (pp30) REVERT: C 695 LYS cc_start: 0.8502 (mptt) cc_final: 0.8093 (pttp) REVERT: C 1063 TRP cc_start: 0.7965 (m-90) cc_final: 0.7751 (m-90) REVERT: C 1095 TYR cc_start: 0.7434 (t80) cc_final: 0.6894 (t80) REVERT: D 467 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8486 (mm) REVERT: D 486 GLU cc_start: 0.7860 (tp30) cc_final: 0.7435 (tp30) REVERT: D 563 GLN cc_start: 0.5536 (mt0) cc_final: 0.4734 (tm-30) REVERT: D 656 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7975 (tmtt) REVERT: D 684 ARG cc_start: 0.8023 (pmm150) cc_final: 0.7685 (mtm-85) REVERT: D 705 GLU cc_start: 0.7942 (mp0) cc_final: 0.7704 (mp0) REVERT: D 713 GLU cc_start: 0.7493 (tt0) cc_final: 0.7238 (tt0) REVERT: D 813 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7578 (pt0) REVERT: D 1032 TRP cc_start: 0.8501 (m100) cc_final: 0.8135 (m-10) REVERT: D 1035 SER cc_start: 0.8026 (p) cc_final: 0.7675 (t) REVERT: D 1077 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.6423 (ptpp) REVERT: D 1202 ASP cc_start: 0.7386 (t70) cc_final: 0.7117 (t0) outliers start: 62 outliers final: 47 residues processed: 335 average time/residue: 0.2686 time to fit residues: 144.3152 Evaluate side-chains 340 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 289 time to evaluate : 2.252 ------------------------------------------------------------------------------- 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 498 LEU 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 B residue 445 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1116 MET 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 693 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain C residue 1191 MET Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19866 Z= 0.273 Angle : 0.575 10.790 26842 Z= 0.301 Chirality : 0.043 0.193 2998 Planarity : 0.003 0.034 3312 Dihedral : 6.310 82.747 2790 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.02 % Allowed : 18.36 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2460 helix: 2.01 (0.14), residues: 1336 sheet: -1.22 (0.43), residues: 142 loop : -1.59 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1063 HIS 0.009 0.002 HIS B 412 PHE 0.017 0.002 PHE B 438 TYR 0.023 0.001 TYR C 523 ARG 0.003 0.000 ARG B1005 *********************** 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 362 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 299 time to evaluate : 2.299 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.7945 (mpt) cc_final: 0.7651 (mtp) REVERT: A 642 GLN cc_start: 0.8294 (pp30) cc_final: 0.8014 (pp30) REVERT: A 695 LYS cc_start: 0.8492 (mptt) cc_final: 0.8188 (pttp) REVERT: A 795 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.9042 (p) REVERT: A 817 LYS cc_start: 0.7296 (mmtp) cc_final: 0.7078 (mttt) REVERT: A 1126 PHE cc_start: 0.7405 (t80) cc_final: 0.7122 (m-80) REVERT: B 563 GLN cc_start: 0.5655 (mt0) cc_final: 0.4711 (tm-30) REVERT: B 656 LYS cc_start: 0.8613 (tttt) cc_final: 0.8272 (tmtt) REVERT: B 684 ARG cc_start: 0.8059 (pmm150) cc_final: 0.7771 (mtm-85) REVERT: B 713 GLU cc_start: 0.7559 (tt0) cc_final: 0.7266 (tt0) REVERT: B 1032 TRP cc_start: 0.8559 (m100) cc_final: 0.8156 (m-10) REVERT: B 1035 SER cc_start: 0.8093 (p) cc_final: 0.7711 (t) REVERT: B 1069 GLU cc_start: 0.6551 (tp30) cc_final: 0.6207 (tm-30) REVERT: C 414 MET cc_start: 0.7892 (mpt) cc_final: 0.7589 (mtp) REVERT: C 642 GLN cc_start: 0.8254 (pp30) cc_final: 0.7963 (pp30) REVERT: C 695 LYS cc_start: 0.8531 (mptt) cc_final: 0.8133 (pttp) REVERT: C 1063 TRP cc_start: 0.7976 (m-90) cc_final: 0.7618 (m-90) REVERT: C 1095 TYR cc_start: 0.7421 (t80) cc_final: 0.6908 (t80) REVERT: D 467 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8473 (mm) REVERT: D 563 GLN cc_start: 0.5594 (mt0) cc_final: 0.4756 (tm-30) REVERT: D 656 LYS cc_start: 0.8465 (ttmt) cc_final: 0.7972 (tmtt) REVERT: D 684 ARG cc_start: 0.8032 (pmm150) cc_final: 0.7685 (mtm-85) REVERT: D 705 GLU cc_start: 0.7969 (mp0) cc_final: 0.7708 (mp0) REVERT: D 713 GLU cc_start: 0.7532 (tt0) cc_final: 0.7237 (tt0) REVERT: D 813 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7571 (pt0) REVERT: D 1032 TRP cc_start: 0.8522 (m100) cc_final: 0.8153 (m-10) REVERT: D 1035 SER cc_start: 0.7973 (p) cc_final: 0.7643 (t) REVERT: D 1077 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6358 (ptpp) REVERT: D 1202 ASP cc_start: 0.7420 (t70) cc_final: 0.7137 (t0) outliers start: 63 outliers final: 54 residues processed: 340 average time/residue: 0.2633 time to fit residues: 144.1683 Evaluate side-chains 344 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 287 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 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 B residue 445 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 1116 MET 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 693 VAL Chi-restraints excluded: chain C residue 759 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 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 536 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1187 ILE 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: 0.5980 chunk 143 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 247 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19866 Z= 0.241 Angle : 0.566 11.899 26842 Z= 0.296 Chirality : 0.042 0.188 2998 Planarity : 0.003 0.033 3312 Dihedral : 6.216 81.453 2790 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.78 % Allowed : 18.98 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2460 helix: 2.06 (0.14), residues: 1338 sheet: -1.25 (0.43), residues: 142 loop : -1.57 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1063 HIS 0.010 0.001 HIS B 412 PHE 0.017 0.001 PHE B 438 TYR 0.022 0.001 TYR C 523 ARG 0.005 0.000 ARG B1005 ********************** 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 349 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 291 time to evaluate : 2.038 Fit side-chains REVERT: A 414 MET cc_start: 0.7927 (mpt) cc_final: 0.7636 (mtp) REVERT: A 642 GLN cc_start: 0.8270 (pp30) cc_final: 0.8017 (pp30) REVERT: A 695 LYS cc_start: 0.8508 (mptt) cc_final: 0.8116 (pttp) REVERT: A 795 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.9054 (p) REVERT: A 1126 PHE cc_start: 0.7324 (t80) cc_final: 0.7048 (m-80) REVERT: B 563 GLN cc_start: 0.5591 (mt0) cc_final: 0.4714 (tm-30) REVERT: B 656 LYS cc_start: 0.8605 (tttt) cc_final: 0.8338 (tmtt) REVERT: B 684 ARG cc_start: 0.8065 (pmm150) cc_final: 0.7769 (mtm-85) REVERT: B 705 GLU cc_start: 0.7982 (mp0) cc_final: 0.7727 (mp0) REVERT: B 713 GLU cc_start: 0.7545 (tt0) cc_final: 0.7249 (tt0) REVERT: B 1032 TRP cc_start: 0.8555 (m100) cc_final: 0.8188 (m-10) REVERT: B 1035 SER cc_start: 0.7998 (p) cc_final: 0.7589 (t) REVERT: B 1069 GLU cc_start: 0.6348 (tp30) cc_final: 0.6134 (tm-30) REVERT: C 414 MET cc_start: 0.7936 (mpt) cc_final: 0.7644 (mtp) REVERT: C 642 GLN cc_start: 0.8244 (pp30) cc_final: 0.7965 (pp30) REVERT: C 695 LYS cc_start: 0.8563 (mptt) cc_final: 0.8126 (pttp) REVERT: C 1063 TRP cc_start: 0.7946 (m-90) cc_final: 0.7582 (m-90) REVERT: C 1095 TYR cc_start: 0.7426 (t80) cc_final: 0.6911 (t80) REVERT: D 563 GLN cc_start: 0.5634 (mt0) cc_final: 0.4815 (tm-30) REVERT: D 656 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7957 (tmtt) REVERT: D 684 ARG cc_start: 0.8026 (pmm150) cc_final: 0.7696 (mtm-85) REVERT: D 705 GLU cc_start: 0.7940 (mp0) cc_final: 0.7701 (mp0) REVERT: D 713 GLU cc_start: 0.7508 (tt0) cc_final: 0.7224 (tt0) REVERT: D 813 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7511 (pt0) REVERT: D 1032 TRP cc_start: 0.8513 (m100) cc_final: 0.8152 (m-10) REVERT: D 1035 SER cc_start: 0.7986 (p) cc_final: 0.7657 (t) REVERT: D 1077 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6350 (ptpp) REVERT: D 1202 ASP cc_start: 0.7436 (t70) cc_final: 0.7164 (t0) outliers start: 58 outliers final: 53 residues processed: 327 average time/residue: 0.2648 time to fit residues: 139.7981 Evaluate side-chains 341 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 286 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 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 B residue 407 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 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 496 MET Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain C residue 1134 ILE Chi-restraints excluded: chain C residue 1135 LEU Chi-restraints excluded: chain C residue 1184 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 1077 LYS Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1185 SER Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 197 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 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 563 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.139837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110041 restraints weight = 30423.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112178 restraints weight = 19760.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112597 restraints weight = 14118.865| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19866 Z= 0.174 Angle : 0.545 12.297 26842 Z= 0.284 Chirality : 0.041 0.197 2998 Planarity : 0.003 0.034 3312 Dihedral : 5.930 77.312 2790 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.30 % Allowed : 19.75 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2460 helix: 2.23 (0.14), residues: 1338 sheet: -1.24 (0.43), residues: 142 loop : -1.55 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1063 HIS 0.010 0.001 HIS B 412 PHE 0.020 0.001 PHE B 438 TYR 0.022 0.001 TYR A1155 ARG 0.005 0.000 ARG B1005 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.43 seconds wall clock time: 74 minutes 1.35 seconds (4441.35 seconds total)