Starting phenix.real_space_refine on Sun Jun 15 06:16:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3x_17398/06_2025/8p3x_17398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3x_17398/06_2025/8p3x_17398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3x_17398/06_2025/8p3x_17398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3x_17398/06_2025/8p3x_17398.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3x_17398/06_2025/8p3x_17398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3x_17398/06_2025/8p3x_17398.cif" } resolution = 3.36 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= -0.001 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 11142 2.51 5 N 2749 2.21 5 O 3023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17035 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2910 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 398, 2899 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 115 Conformer: "B" Number of residues, atoms: 398, 2899 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 115 bond proxies already assigned to first conformer: 2950 Chain: "B" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2886 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 384} Chain breaks: 4 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2881 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 384} Chain breaks: 4 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 2883 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 2872 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 382} Chain breaks: 3 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 116 Conformer: "B" Number of residues, atoms: 395, 2872 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 382} Chain breaks: 3 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 116 bond proxies already assigned to first conformer: 2925 Chain: "E" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1358 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 Time building chain proxies: 12.01, per 1000 atoms: 0.71 Number of scatterers: 17035 At special positions: 0 Unit cell: (115.64, 144.55, 145.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 121 16.00 O 3023 8.00 N 2749 7.00 C 11142 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=2.00 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.01 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.05 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.05 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.04 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.04 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.05 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.10 Conformation dependent library (CDL) restraints added in 2.7 seconds 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 28 sheets defined 60.8% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.839A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.634A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.790A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.842A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 628 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.600A pdb=" N LEU A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 820 removed outlier: 3.635A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.673A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.780A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.647A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.639A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 769 through 771 No H-bonds generated for 'chain 'B' and resid 769 through 771' Processing helix chain 'B' and resid 792 through 822 removed outlier: 3.548A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 822 " --> pdb=" O SER B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.615A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.764A 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 522 through 546 removed outlier: 3.531A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.669A pdb=" N GLU C 550 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 547 through 551' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 628 removed outlier: 3.567A pdb=" N ARG C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.652A pdb=" N LEU C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.763A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.014A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.622A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.769A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.845A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.706A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 624 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.503A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 823 removed outlier: 3.798A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 823 " --> pdb=" O ARG D 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 124 Processing helix chain 'E' and resid 133 through 160 removed outlier: 3.799A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 Processing helix chain 'F' and resid 6 through 28 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 105 through 127 removed outlier: 3.968A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 Processing helix chain 'F' and resid 177 through 209 Processing helix chain 'G' and resid 7 through 30 removed outlier: 3.692A pdb=" N LEU G 11 " --> pdb=" O GLY G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 127 removed outlier: 4.113A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 161 Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 3.931A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 133 through 161 removed outlier: 3.582A pdb=" N ALA H 161 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 209 removed outlier: 3.967A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 394 through 399 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 451 through 453 removed outlier: 3.611A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.469A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.469A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 399 Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.475A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.475A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 394 through 399 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 490 through 491 Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.485A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.485A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 395 through 399 removed outlier: 6.701A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 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 646 through 648 removed outlier: 6.408A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.408A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC5, first strand: chain 'F' and resid 34 through 35 removed outlier: 4.129A pdb=" N SER F 175 " --> pdb=" O TYR F 35 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.767A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC9, first strand: chain 'H' and resid 36 through 38 Processing sheet with id=AD1, first strand: chain 'H' and resid 65 through 67 1124 hydrogen bonds defined for protein. 3282 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: 5.26 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2640 1.31 - 1.44: 5000 1.44 - 1.57: 9588 1.57 - 1.70: 0 1.70 - 1.83: 194 Bond restraints: 17422 Sorted by residual: bond pdb=" C APHE D 574 " pdb=" N ASN D 575 " ideal model delta sigma weight residual 1.335 1.463 -0.127 1.38e-02 5.25e+03 8.54e+01 bond pdb=" C BPHE D 574 " pdb=" N ASN D 575 " ideal model delta sigma weight residual 1.334 1.468 -0.133 1.46e-02 4.69e+03 8.36e+01 bond pdb=" C ASN A 709 " pdb=" O ASN A 709 " ideal model delta sigma weight residual 1.237 1.306 -0.069 1.16e-02 7.43e+03 3.55e+01 bond pdb=" CA SER A 592 " pdb=" CB SER A 592 " ideal model delta sigma weight residual 1.535 1.472 0.063 1.21e-02 6.83e+03 2.68e+01 bond pdb=" C ILE A 573 " pdb=" N APHE A 574 " ideal model delta sigma weight residual 1.335 1.404 -0.070 1.36e-02 5.41e+03 2.62e+01 ... (remaining 17417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 19816 2.26 - 4.53: 3557 4.53 - 6.79: 270 6.79 - 9.05: 13 9.05 - 11.32: 4 Bond angle restraints: 23660 Sorted by residual: angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" CB ILE A 712 " ideal model delta sigma weight residual 110.54 99.22 11.32 1.36e+00 5.41e-01 6.93e+01 angle pdb=" N GLU A 772 " pdb=" CA GLU A 772 " pdb=" C GLU A 772 " ideal model delta sigma weight residual 113.61 102.50 11.11 1.50e+00 4.44e-01 5.48e+01 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 105.69 8.19 1.23e+00 6.61e-01 4.44e+01 angle pdb=" N LEU C 803 " pdb=" CA LEU C 803 " pdb=" C LEU C 803 " ideal model delta sigma weight residual 111.82 104.39 7.43 1.16e+00 7.43e-01 4.10e+01 angle pdb=" N LEU D 620 " pdb=" CA LEU D 620 " pdb=" C LEU D 620 " ideal model delta sigma weight residual 111.07 104.25 6.82 1.07e+00 8.73e-01 4.06e+01 ... (remaining 23655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8930 17.77 - 35.53: 878 35.53 - 53.30: 152 53.30 - 71.06: 20 71.06 - 88.83: 13 Dihedral angle restraints: 9993 sinusoidal: 3435 harmonic: 6558 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 24.05 68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 38.89 54.11 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 39.54 53.46 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 9990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 921 0.065 - 0.130: 1006 0.130 - 0.194: 628 0.194 - 0.259: 177 0.259 - 0.324: 13 Chirality restraints: 2745 Sorted by residual: chirality pdb=" CA ILE A 712 " pdb=" N ILE A 712 " pdb=" C ILE A 712 " pdb=" CB ILE A 712 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA GLU A 710 " pdb=" N GLU A 710 " pdb=" C GLU A 710 " pdb=" CB GLU A 710 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA CYS C 589 " pdb=" N CYS C 589 " pdb=" C CYS C 589 " pdb=" CB CYS C 589 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2742 not shown) Planarity restraints: 2906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BPHE D 574 " -0.036 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" C BPHE D 574 " 0.119 2.00e-02 2.50e+03 pdb=" O BPHE D 574 " -0.046 2.00e-02 2.50e+03 pdb=" N ASN D 575 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 819 " 0.569 9.50e-02 1.11e+02 2.55e-01 3.97e+01 pdb=" NE ARG C 819 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG C 819 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 819 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 819 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 420 " 0.520 9.50e-02 1.11e+02 2.33e-01 3.32e+01 pdb=" NE ARG B 420 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 420 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 420 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 420 " 0.019 2.00e-02 2.50e+03 ... (remaining 2903 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4188 2.77 - 3.30: 17633 3.30 - 3.83: 27176 3.83 - 4.37: 34067 4.37 - 4.90: 54990 Nonbonded interactions: 138054 Sorted by model distance: nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.236 3.040 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.250 3.120 nonbonded pdb=" N VAL D 395 " pdb=" O LYS D 439 " model vdw 2.261 3.120 nonbonded pdb=" O ASP B 427 " pdb=" OE1 GLU B 431 " model vdw 2.291 3.040 nonbonded pdb=" O ASP A 427 " pdb=" OE1 GLU A 431 " model vdw 2.294 3.040 ... (remaining 138049 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 393 through 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 through 573 or resid 575 through 593 o \ r (resid 594 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 95 through 626 or resid 635 through 773 or resid 785 through 812 or (resid 813 a \ nd (name N or name CA or name C or name O or name CB )) or resid 814 through 818 \ or (resid 819 through 823 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'B' and (resid 393 through 506 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 549 or (resid 550 and (name N \ or name CA or name C or name O or name CB )) or resid 551 or (resid 569 and (nam \ e N or name CA or name C or name O or name CB )) or resid 570 through 573 or res \ id 575 or (resid 576 and (name N or name CA or name C or name O or name CB )) or \ resid 577 through 593 or (resid 594 and (name N or name CA or name C or name O \ or name CB )) or resid 595 through 626 or resid 635 through 773 or resid 785 thr \ ough 823)) selection = (chain 'C' and (resid 393 through 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 626 or resid 635 \ through 812 or (resid 813 and (name N or name CA or name C or name O or name CB \ )) or resid 814 through 818 or (resid 819 through 823 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'D' and (resid 393 through 506 or resid 511 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 569 \ and (name N or name CA or name C or name O or name CB )) or resid 570 through 5 \ 73 or resid 575 or (resid 576 and (name N or name CA or name C or name O or name \ CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C o \ r name O or name CB )) or resid 595 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 84 or resid 93 through \ 161 or resid 173 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 56 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 84 or resid 93 through \ 161 or resid 173 through 210)) selection = (chain 'H' and (resid 5 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 42 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 161 or resid 173 throu \ gh 210)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 40.750 Find NCS groups from input model: 0.860 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 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 : 0.013 0.133 17434 Z= 0.932 Angle : 1.657 11.319 23684 Z= 1.252 Chirality : 0.115 0.324 2745 Planarity : 0.014 0.255 2906 Dihedral : 14.277 88.829 5765 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.36 % Favored : 95.41 % Rotamer: Outliers : 1.68 % Allowed : 7.13 % Favored : 91.20 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 2229 helix: -0.38 (0.12), residues: 1304 sheet: -1.98 (0.37), residues: 145 loop : -2.01 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP A 767 HIS 0.009 0.002 HIS E 60 PHE 0.032 0.004 PHE A 667 TYR 0.041 0.004 TYR A 647 ARG 0.014 0.001 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.15394 ( 1108) hydrogen bonds : angle 5.88658 ( 3282) SS BOND : bond 0.01615 ( 12) SS BOND : angle 2.24462 ( 24) covalent geometry : bond 0.01303 (17422) covalent geometry : angle 1.65641 (23660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 405 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.8956 (p0) cc_final: 0.8645 (p0) REVERT: A 594 ARG cc_start: 0.9599 (mtm-85) cc_final: 0.9316 (mtp85) REVERT: A 651 ASP cc_start: 0.3695 (p0) cc_final: 0.3107 (p0) REVERT: A 674 MET cc_start: 0.5429 (mtm) cc_final: 0.4769 (mtt) REVERT: A 819 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8749 (ptm-80) REVERT: C 633 ILE cc_start: -0.0215 (OUTLIER) cc_final: -0.0891 (pt) REVERT: D 519 ASP cc_start: 0.9464 (m-30) cc_final: 0.9203 (m-30) REVERT: E 78 LYS cc_start: 0.9264 (pttt) cc_final: 0.8878 (pttm) REVERT: E 81 ASP cc_start: 0.9271 (t0) cc_final: 0.9004 (p0) REVERT: E 192 MET cc_start: 0.8857 (mtt) cc_final: 0.8582 (mmt) REVERT: E 200 MET cc_start: 0.9334 (mtm) cc_final: 0.9101 (mtm) REVERT: F 24 MET cc_start: 0.9363 (tpt) cc_final: 0.9076 (tpt) REVERT: F 99 ARG cc_start: 0.9004 (tpp80) cc_final: 0.8778 (mmm-85) REVERT: F 117 MET cc_start: 0.8831 (mmm) cc_final: 0.8559 (mmm) REVERT: F 192 MET cc_start: 0.8424 (mtt) cc_final: 0.8077 (mmt) REVERT: F 207 GLN cc_start: 0.9419 (tt0) cc_final: 0.9028 (tm-30) REVERT: G 10 MET cc_start: 0.8778 (tpt) cc_final: 0.8424 (tpp) REVERT: G 24 MET cc_start: 0.8924 (tpt) cc_final: 0.8373 (tpt) REVERT: G 99 ARG cc_start: 0.9318 (mtt-85) cc_final: 0.8795 (mtm-85) REVERT: H 24 MET cc_start: 0.9238 (tpt) cc_final: 0.9009 (tpt) REVERT: H 58 MET cc_start: 0.9375 (mmp) cc_final: 0.9128 (mmp) REVERT: H 95 GLU cc_start: 0.9545 (tm-30) cc_final: 0.9264 (pm20) outliers start: 28 outliers final: 6 residues processed: 425 average time/residue: 0.3514 time to fit residues: 209.4259 Evaluate side-chains 246 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 238 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain F residue 58 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 203 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 569 ASN B 619 ASN D 461 ASN D 619 ASN E 9 GLN E 82 HIS E 160 ASN F 82 HIS F 132 HIS F 205 HIS G 9 GLN G 205 HIS H 79 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.135798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.080704 restraints weight = 60291.504| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.07 r_work: 0.3039 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17434 Z= 0.143 Angle : 0.620 11.544 23684 Z= 0.332 Chirality : 0.042 0.266 2745 Planarity : 0.004 0.041 2906 Dihedral : 4.661 56.788 2451 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.16 % Allowed : 14.79 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % 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: 0.93 (0.18), residues: 2229 helix: 1.99 (0.14), residues: 1325 sheet: -1.51 (0.38), residues: 154 loop : -1.47 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 671 HIS 0.005 0.001 HIS F 82 PHE 0.014 0.001 PHE G 73 TYR 0.015 0.001 TYR D 469 ARG 0.007 0.001 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 1108) hydrogen bonds : angle 4.11339 ( 3282) SS BOND : bond 0.00408 ( 12) SS BOND : angle 1.46092 ( 24) covalent geometry : bond 0.00298 (17422) covalent geometry : angle 0.61828 (23660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.6321 (ttm) cc_final: 0.6043 (ttp) REVERT: A 594 ARG cc_start: 0.9108 (mtm-85) cc_final: 0.8867 (mtp85) REVERT: A 674 MET cc_start: 0.6493 (mtm) cc_final: 0.5816 (mtt) REVERT: B 673 TYR cc_start: 0.7677 (t80) cc_final: 0.7297 (t80) REVERT: B 684 ARG cc_start: 0.4565 (tmt170) cc_final: 0.4070 (tmt170) REVERT: B 721 MET cc_start: 0.5200 (ptt) cc_final: 0.4914 (ptp) REVERT: C 408 MET cc_start: 0.5888 (mmt) cc_final: 0.5440 (mmm) REVERT: C 813 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8909 (tm-30) REVERT: D 407 MET cc_start: 0.9197 (tpp) cc_final: 0.8769 (mtm) REVERT: D 519 ASP cc_start: 0.9062 (m-30) cc_final: 0.8757 (m-30) REVERT: D 590 ASP cc_start: 0.8689 (t70) cc_final: 0.8417 (t0) REVERT: E 37 ARG cc_start: 0.8885 (ttp80) cc_final: 0.8646 (ttp80) REVERT: E 78 LYS cc_start: 0.9070 (pttt) cc_final: 0.8598 (pttm) REVERT: E 176 TYR cc_start: 0.8791 (m-80) cc_final: 0.8400 (m-80) REVERT: E 195 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.8986 (t) REVERT: F 10 MET cc_start: 0.8364 (mmm) cc_final: 0.7602 (tpp) REVERT: F 58 MET cc_start: 0.9179 (tpp) cc_final: 0.8671 (mmp) REVERT: F 99 ARG cc_start: 0.8712 (tpp80) cc_final: 0.8316 (mmm-85) REVERT: F 160 ASN cc_start: 0.8671 (m-40) cc_final: 0.8253 (m110) REVERT: F 174 TYR cc_start: 0.8049 (p90) cc_final: 0.6862 (p90) REVERT: F 185 LEU cc_start: 0.9204 (tp) cc_final: 0.8967 (tp) REVERT: F 192 MET cc_start: 0.8611 (mtt) cc_final: 0.8279 (mmp) REVERT: F 207 GLN cc_start: 0.9172 (tt0) cc_final: 0.8690 (tm-30) REVERT: G 24 MET cc_start: 0.9269 (tpt) cc_final: 0.8436 (tpt) REVERT: G 56 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8874 (mm-30) REVERT: G 81 ASP cc_start: 0.8270 (t0) cc_final: 0.7972 (t0) REVERT: G 99 ARG cc_start: 0.8743 (mtt-85) cc_final: 0.8184 (mtm180) REVERT: H 31 ASP cc_start: 0.8269 (m-30) cc_final: 0.7936 (m-30) outliers start: 36 outliers final: 16 residues processed: 312 average time/residue: 0.3686 time to fit residues: 169.1805 Evaluate side-chains 250 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 217 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 chunk 147 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 202 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 619 ASN D 619 ASN E 9 GLN E 72 ASN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 205 HIS G 205 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.133942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.082262 restraints weight = 75123.394| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 6.32 r_work: 0.2907 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17434 Z= 0.158 Angle : 0.592 12.252 23684 Z= 0.312 Chirality : 0.041 0.232 2745 Planarity : 0.004 0.040 2906 Dihedral : 3.975 51.176 2435 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.11 % Allowed : 15.75 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.19), residues: 2229 helix: 2.58 (0.15), residues: 1330 sheet: -1.26 (0.39), residues: 167 loop : -1.27 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 671 HIS 0.009 0.001 HIS E 82 PHE 0.013 0.001 PHE G 73 TYR 0.016 0.001 TYR D 732 ARG 0.006 0.001 ARG D 586 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 1108) hydrogen bonds : angle 4.02648 ( 3282) SS BOND : bond 0.00377 ( 12) SS BOND : angle 1.17455 ( 24) covalent geometry : bond 0.00359 (17422) covalent geometry : angle 0.59093 (23660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.6733 (ttm) cc_final: 0.5825 (tmm) REVERT: A 497 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.7855 (t) REVERT: A 594 ARG cc_start: 0.9328 (mtm-85) cc_final: 0.9050 (mtp85) REVERT: A 674 MET cc_start: 0.6544 (mtm) cc_final: 0.5903 (mtt) REVERT: B 503 MET cc_start: 0.7185 (tmm) cc_final: 0.6491 (tmm) REVERT: B 570 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8444 (mp0) REVERT: B 673 TYR cc_start: 0.7832 (t80) cc_final: 0.7527 (t80) REVERT: B 674 MET cc_start: 0.7920 (tpp) cc_final: 0.7675 (tpp) REVERT: B 684 ARG cc_start: 0.4483 (tmt170) cc_final: 0.3981 (tmt170) REVERT: B 721 MET cc_start: 0.5482 (ptt) cc_final: 0.5010 (ptp) REVERT: C 813 GLU cc_start: 0.9318 (tm-30) cc_final: 0.9038 (tm-30) REVERT: D 407 MET cc_start: 0.9168 (tpp) cc_final: 0.8704 (mtm) REVERT: D 408 MET cc_start: 0.8935 (mmm) cc_final: 0.7982 (tpt) REVERT: D 503 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6525 (mmp) REVERT: D 519 ASP cc_start: 0.9224 (m-30) cc_final: 0.8909 (m-30) REVERT: D 590 ASP cc_start: 0.8806 (t70) cc_final: 0.8482 (t0) REVERT: E 10 MET cc_start: 0.8764 (mmm) cc_final: 0.8451 (tpp) REVERT: E 78 LYS cc_start: 0.9100 (pttt) cc_final: 0.8634 (pttm) REVERT: E 160 ASN cc_start: 0.8546 (m-40) cc_final: 0.8176 (t0) REVERT: F 58 MET cc_start: 0.9223 (tpp) cc_final: 0.8785 (mmp) REVERT: F 81 ASP cc_start: 0.8982 (t0) cc_final: 0.8644 (t0) REVERT: F 110 LEU cc_start: 0.8915 (tp) cc_final: 0.8615 (tp) REVERT: F 126 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8724 (mm-30) REVERT: F 160 ASN cc_start: 0.8637 (m-40) cc_final: 0.8152 (m110) REVERT: F 192 MET cc_start: 0.8811 (mtt) cc_final: 0.8459 (mmp) REVERT: F 207 GLN cc_start: 0.9128 (tt0) cc_final: 0.8726 (tm-30) REVERT: G 10 MET cc_start: 0.8898 (mmm) cc_final: 0.8441 (tpp) REVERT: G 25 THR cc_start: 0.9593 (t) cc_final: 0.9376 (p) REVERT: G 81 ASP cc_start: 0.8446 (t0) cc_final: 0.8181 (t0) REVERT: G 99 ARG cc_start: 0.8844 (mtt-85) cc_final: 0.8271 (mtm180) REVERT: H 31 ASP cc_start: 0.8257 (m-30) cc_final: 0.7827 (m-30) REVERT: H 35 TYR cc_start: 0.8278 (m-80) cc_final: 0.7794 (m-80) outliers start: 52 outliers final: 29 residues processed: 285 average time/residue: 0.3234 time to fit residues: 136.2181 Evaluate side-chains 251 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 40.0000 chunk 122 optimal weight: 8.9990 chunk 109 optimal weight: 50.0000 chunk 39 optimal weight: 40.0000 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 111 optimal weight: 40.0000 chunk 137 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 569 ASN B 619 ASN D 619 ASN D 791 ASN F 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.131617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079965 restraints weight = 81958.211| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 6.23 r_work: 0.2852 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17434 Z= 0.203 Angle : 0.613 11.407 23684 Z= 0.323 Chirality : 0.041 0.222 2745 Planarity : 0.004 0.040 2906 Dihedral : 3.935 40.638 2435 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.59 % Allowed : 17.31 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 2229 helix: 2.63 (0.15), residues: 1337 sheet: -0.90 (0.42), residues: 161 loop : -1.16 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 671 HIS 0.030 0.002 HIS G 205 PHE 0.015 0.002 PHE G 73 TYR 0.016 0.001 TYR D 732 ARG 0.006 0.001 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 1108) hydrogen bonds : angle 4.08973 ( 3282) SS BOND : bond 0.00376 ( 12) SS BOND : angle 1.53184 ( 24) covalent geometry : bond 0.00469 (17422) covalent geometry : angle 0.61156 (23660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.6769 (ttm) cc_final: 0.5898 (tmm) REVERT: A 594 ARG cc_start: 0.9418 (mtm-85) cc_final: 0.9079 (mtp85) REVERT: A 674 MET cc_start: 0.6554 (mtm) cc_final: 0.5900 (mtt) REVERT: B 431 GLU cc_start: 0.6963 (pm20) cc_final: 0.6649 (pm20) REVERT: B 503 MET cc_start: 0.7180 (tmm) cc_final: 0.6824 (tmm) REVERT: B 570 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8505 (mp0) REVERT: B 673 TYR cc_start: 0.7907 (t80) cc_final: 0.7590 (t80) REVERT: B 674 MET cc_start: 0.8053 (tpp) cc_final: 0.7740 (tpp) REVERT: B 683 VAL cc_start: 0.5732 (OUTLIER) cc_final: 0.5493 (t) REVERT: B 684 ARG cc_start: 0.4707 (tmt170) cc_final: 0.4237 (tmt170) REVERT: B 721 MET cc_start: 0.5513 (ptt) cc_final: 0.5255 (ptp) REVERT: C 813 GLU cc_start: 0.9341 (tm-30) cc_final: 0.9066 (tm-30) REVERT: D 503 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.6677 (mmm) REVERT: D 590 ASP cc_start: 0.8813 (t70) cc_final: 0.8470 (t0) REVERT: E 160 ASN cc_start: 0.8715 (m-40) cc_final: 0.8256 (t0) REVERT: F 58 MET cc_start: 0.9198 (tpp) cc_final: 0.8733 (mmp) REVERT: F 81 ASP cc_start: 0.9015 (t0) cc_final: 0.8694 (t0) REVERT: F 126 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8730 (mm-30) REVERT: F 192 MET cc_start: 0.8778 (mtt) cc_final: 0.8451 (mmp) REVERT: F 207 GLN cc_start: 0.9220 (tt0) cc_final: 0.8803 (tm-30) REVERT: G 10 MET cc_start: 0.9002 (mmm) cc_final: 0.8308 (tpp) REVERT: G 14 THR cc_start: 0.9361 (t) cc_final: 0.8942 (p) REVERT: G 25 THR cc_start: 0.9596 (t) cc_final: 0.9369 (p) REVERT: G 69 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8646 (pp) REVERT: G 81 ASP cc_start: 0.8510 (t0) cc_final: 0.8240 (t0) REVERT: G 99 ARG cc_start: 0.8856 (mtt-85) cc_final: 0.8270 (mtm180) REVERT: H 31 ASP cc_start: 0.8185 (m-30) cc_final: 0.7781 (m-30) REVERT: H 35 TYR cc_start: 0.8326 (m-80) cc_final: 0.7595 (m-80) outliers start: 60 outliers final: 38 residues processed: 271 average time/residue: 0.3588 time to fit residues: 144.0177 Evaluate side-chains 251 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 33 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 175 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 619 ASN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.134357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.082294 restraints weight = 78642.047| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 6.34 r_work: 0.2925 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17434 Z= 0.119 Angle : 0.579 11.688 23684 Z= 0.296 Chirality : 0.040 0.239 2745 Planarity : 0.003 0.042 2906 Dihedral : 3.763 27.814 2435 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.93 % Allowed : 18.56 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2229 helix: 2.79 (0.15), residues: 1335 sheet: -0.83 (0.41), residues: 168 loop : -1.06 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 671 HIS 0.005 0.001 HIS E 82 PHE 0.015 0.001 PHE G 73 TYR 0.013 0.001 TYR D 702 ARG 0.008 0.001 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1108) hydrogen bonds : angle 3.84131 ( 3282) SS BOND : bond 0.00363 ( 12) SS BOND : angle 1.45059 ( 24) covalent geometry : bond 0.00264 (17422) covalent geometry : angle 0.57791 (23660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.6611 (ttm) cc_final: 0.5780 (tmm) REVERT: A 497 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7801 (t) REVERT: A 674 MET cc_start: 0.6542 (mtm) cc_final: 0.5892 (mtt) REVERT: B 496 MET cc_start: 0.3368 (ppp) cc_final: 0.3097 (ppp) REVERT: B 503 MET cc_start: 0.7406 (tmm) cc_final: 0.6738 (tmm) REVERT: B 570 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8503 (mp0) REVERT: B 673 TYR cc_start: 0.7931 (t80) cc_final: 0.7554 (t80) REVERT: B 674 MET cc_start: 0.8216 (tpp) cc_final: 0.7958 (tpp) REVERT: B 684 ARG cc_start: 0.4647 (tmt170) cc_final: 0.4132 (tmt170) REVERT: C 408 MET cc_start: 0.6411 (mmt) cc_final: 0.5909 (mmm) REVERT: C 708 MET cc_start: 0.8718 (mmt) cc_final: 0.8293 (mtm) REVERT: C 811 LEU cc_start: 0.9423 (mt) cc_final: 0.9175 (mm) REVERT: D 407 MET cc_start: 0.8262 (mmm) cc_final: 0.7813 (mmm) REVERT: D 408 MET cc_start: 0.8805 (mmm) cc_final: 0.7906 (tpt) REVERT: D 503 MET cc_start: 0.7614 (tpp) cc_final: 0.6699 (mmm) REVERT: D 590 ASP cc_start: 0.8731 (t70) cc_final: 0.8411 (t0) REVERT: D 688 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8152 (pt0) REVERT: D 787 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9302 (mp) REVERT: E 10 MET cc_start: 0.8616 (mmm) cc_final: 0.8214 (tpt) REVERT: E 78 LYS cc_start: 0.8917 (pttt) cc_final: 0.8509 (pttm) REVERT: E 160 ASN cc_start: 0.8667 (m-40) cc_final: 0.8342 (t0) REVERT: F 81 ASP cc_start: 0.9122 (t0) cc_final: 0.8889 (t0) REVERT: F 110 LEU cc_start: 0.8979 (tp) cc_final: 0.8598 (tp) REVERT: F 160 ASN cc_start: 0.8660 (m-40) cc_final: 0.8288 (m110) REVERT: F 185 LEU cc_start: 0.9288 (tp) cc_final: 0.9030 (tp) REVERT: F 192 MET cc_start: 0.8751 (mtt) cc_final: 0.8400 (mmp) REVERT: F 207 GLN cc_start: 0.9124 (tt0) cc_final: 0.8753 (tm-30) REVERT: G 10 MET cc_start: 0.8850 (mmm) cc_final: 0.8188 (tpp) REVERT: G 14 THR cc_start: 0.9432 (t) cc_final: 0.9080 (p) REVERT: G 25 THR cc_start: 0.9546 (t) cc_final: 0.9327 (p) REVERT: G 69 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7999 (pp) REVERT: G 81 ASP cc_start: 0.8523 (t0) cc_final: 0.8292 (t0) REVERT: G 99 ARG cc_start: 0.8834 (mtt-85) cc_final: 0.8258 (mtm180) REVERT: H 31 ASP cc_start: 0.8170 (m-30) cc_final: 0.7950 (m-30) REVERT: H 35 TYR cc_start: 0.8241 (m-80) cc_final: 0.7614 (m-80) outliers start: 49 outliers final: 31 residues processed: 288 average time/residue: 0.4067 time to fit residues: 174.6765 Evaluate side-chains 257 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain D residue 787 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 95 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 43 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 163 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 127 optimal weight: 0.1980 chunk 188 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN B 619 ASN F 205 HIS G 205 HIS H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.130537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078747 restraints weight = 67751.031| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 5.96 r_work: 0.2870 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17434 Z= 0.226 Angle : 0.644 11.363 23684 Z= 0.332 Chirality : 0.041 0.223 2745 Planarity : 0.004 0.043 2906 Dihedral : 3.857 18.929 2434 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.41 % Allowed : 19.10 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 2229 helix: 2.64 (0.15), residues: 1344 sheet: -0.72 (0.41), residues: 171 loop : -1.00 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 671 HIS 0.023 0.002 HIS G 205 PHE 0.015 0.002 PHE G 73 TYR 0.017 0.001 TYR C 523 ARG 0.005 0.001 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 1108) hydrogen bonds : angle 4.09741 ( 3282) SS BOND : bond 0.00608 ( 12) SS BOND : angle 1.36549 ( 24) covalent geometry : bond 0.00521 (17422) covalent geometry : angle 0.64249 (23660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 227 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.6995 (ttm) cc_final: 0.6007 (tmm) REVERT: A 674 MET cc_start: 0.6406 (mtm) cc_final: 0.5718 (mtt) REVERT: B 408 MET cc_start: 0.8049 (tpt) cc_final: 0.6863 (tpt) REVERT: B 496 MET cc_start: 0.2896 (ppp) cc_final: 0.2599 (ppp) REVERT: B 503 MET cc_start: 0.7536 (tmm) cc_final: 0.6895 (tmm) REVERT: B 673 TYR cc_start: 0.7857 (t80) cc_final: 0.7496 (t80) REVERT: B 674 MET cc_start: 0.8266 (tpp) cc_final: 0.7980 (tpp) REVERT: B 684 ARG cc_start: 0.4697 (tmt170) cc_final: 0.4328 (tmt170) REVERT: B 721 MET cc_start: 0.5794 (ptt) cc_final: 0.5066 (ptp) REVERT: C 811 LEU cc_start: 0.9485 (mt) cc_final: 0.9263 (mm) REVERT: D 407 MET cc_start: 0.8520 (mmm) cc_final: 0.8059 (mmm) REVERT: D 408 MET cc_start: 0.8888 (mmm) cc_final: 0.8281 (tpt) REVERT: D 503 MET cc_start: 0.7632 (tpp) cc_final: 0.6974 (mmp) REVERT: D 524 GLU cc_start: 0.8983 (mp0) cc_final: 0.8629 (mp0) REVERT: D 590 ASP cc_start: 0.8703 (t70) cc_final: 0.8351 (t0) REVERT: E 10 MET cc_start: 0.8516 (mmm) cc_final: 0.8062 (tpt) REVERT: E 78 LYS cc_start: 0.9023 (pttt) cc_final: 0.8638 (pttm) REVERT: E 160 ASN cc_start: 0.8805 (m-40) cc_final: 0.8451 (t0) REVERT: E 176 TYR cc_start: 0.9020 (m-80) cc_final: 0.8452 (m-80) REVERT: F 61 SER cc_start: 0.9510 (t) cc_final: 0.9274 (p) REVERT: F 81 ASP cc_start: 0.9097 (t0) cc_final: 0.8864 (t0) REVERT: F 156 TYR cc_start: 0.9550 (t80) cc_final: 0.9311 (t80) REVERT: F 160 ASN cc_start: 0.8796 (m-40) cc_final: 0.8236 (m110) REVERT: F 192 MET cc_start: 0.8777 (mtt) cc_final: 0.8447 (mmp) REVERT: F 207 GLN cc_start: 0.9184 (tt0) cc_final: 0.8796 (tm-30) REVERT: G 10 MET cc_start: 0.8927 (mmm) cc_final: 0.8479 (tpp) REVERT: G 25 THR cc_start: 0.9614 (t) cc_final: 0.9399 (p) REVERT: G 58 MET cc_start: 0.8322 (tpp) cc_final: 0.8059 (mmm) REVERT: G 81 ASP cc_start: 0.8455 (t0) cc_final: 0.8195 (t0) REVERT: G 99 ARG cc_start: 0.8889 (mtt-85) cc_final: 0.8335 (mtm180) REVERT: H 31 ASP cc_start: 0.8353 (m-30) cc_final: 0.8145 (m-30) REVERT: H 35 TYR cc_start: 0.8355 (m-80) cc_final: 0.7679 (m-80) outliers start: 57 outliers final: 44 residues processed: 267 average time/residue: 0.3092 time to fit residues: 121.0434 Evaluate side-chains 261 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 172 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 117 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN F 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.131881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080263 restraints weight = 81578.512| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 5.84 r_work: 0.2897 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17434 Z= 0.154 Angle : 0.609 12.133 23684 Z= 0.309 Chirality : 0.040 0.220 2745 Planarity : 0.003 0.044 2906 Dihedral : 3.785 18.150 2434 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.99 % Allowed : 19.94 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2229 helix: 2.72 (0.15), residues: 1344 sheet: -0.67 (0.41), residues: 169 loop : -0.98 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 671 HIS 0.005 0.001 HIS E 82 PHE 0.013 0.001 PHE G 73 TYR 0.015 0.001 TYR D 702 ARG 0.004 0.001 ARG D 586 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1108) hydrogen bonds : angle 3.91325 ( 3282) SS BOND : bond 0.00396 ( 12) SS BOND : angle 1.10547 ( 24) covalent geometry : bond 0.00354 (17422) covalent geometry : angle 0.60809 (23660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.6954 (ttm) cc_final: 0.5963 (tmm) REVERT: A 674 MET cc_start: 0.6261 (mtm) cc_final: 0.5653 (mtt) REVERT: B 496 MET cc_start: 0.2878 (ppp) cc_final: 0.2612 (ppp) REVERT: B 503 MET cc_start: 0.7456 (tmm) cc_final: 0.6891 (tmm) REVERT: B 673 TYR cc_start: 0.7848 (t80) cc_final: 0.7474 (t80) REVERT: B 674 MET cc_start: 0.8191 (tpp) cc_final: 0.7877 (tpp) REVERT: B 683 VAL cc_start: 0.5700 (OUTLIER) cc_final: 0.5245 (t) REVERT: B 684 ARG cc_start: 0.4607 (tmt170) cc_final: 0.4054 (tmt170) REVERT: B 721 MET cc_start: 0.5730 (ptt) cc_final: 0.5002 (ptp) REVERT: D 407 MET cc_start: 0.8843 (mmm) cc_final: 0.8464 (mmm) REVERT: D 408 MET cc_start: 0.8907 (mmm) cc_final: 0.8297 (tpt) REVERT: D 424 TYR cc_start: 0.8238 (t80) cc_final: 0.7615 (m-80) REVERT: D 503 MET cc_start: 0.7747 (tpp) cc_final: 0.7046 (mmp) REVERT: D 524 GLU cc_start: 0.8996 (mp0) cc_final: 0.8701 (mp0) REVERT: D 590 ASP cc_start: 0.8723 (t70) cc_final: 0.8386 (t0) REVERT: E 10 MET cc_start: 0.8459 (mmm) cc_final: 0.8028 (tpt) REVERT: E 78 LYS cc_start: 0.8946 (pttt) cc_final: 0.8589 (pttm) REVERT: E 160 ASN cc_start: 0.8845 (m-40) cc_final: 0.8464 (t0) REVERT: F 61 SER cc_start: 0.9462 (t) cc_final: 0.9230 (p) REVERT: F 81 ASP cc_start: 0.9060 (t0) cc_final: 0.8837 (t0) REVERT: F 156 TYR cc_start: 0.9566 (t80) cc_final: 0.9216 (t80) REVERT: F 160 ASN cc_start: 0.8664 (m-40) cc_final: 0.7830 (m-40) REVERT: F 192 MET cc_start: 0.8760 (mtt) cc_final: 0.8408 (mmp) REVERT: F 207 GLN cc_start: 0.9185 (tt0) cc_final: 0.8835 (tm-30) REVERT: G 10 MET cc_start: 0.8893 (mmm) cc_final: 0.8469 (tpp) REVERT: G 25 THR cc_start: 0.9571 (t) cc_final: 0.9341 (p) REVERT: G 81 ASP cc_start: 0.8456 (t0) cc_final: 0.8212 (t0) REVERT: G 99 ARG cc_start: 0.8803 (mtt-85) cc_final: 0.8171 (mtm-85) REVERT: H 6 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7836 (ptm-80) REVERT: H 31 ASP cc_start: 0.8347 (m-30) cc_final: 0.8136 (m-30) REVERT: H 35 TYR cc_start: 0.8302 (m-80) cc_final: 0.7606 (m-80) outliers start: 50 outliers final: 39 residues processed: 268 average time/residue: 0.3050 time to fit residues: 121.7003 Evaluate side-chains 265 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 106 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 183 optimal weight: 0.0010 chunk 143 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 69 optimal weight: 50.0000 chunk 40 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN H 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.131228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.079903 restraints weight = 75658.712| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 5.01 r_work: 0.2909 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17434 Z= 0.165 Angle : 0.619 12.358 23684 Z= 0.314 Chirality : 0.040 0.220 2745 Planarity : 0.003 0.047 2906 Dihedral : 3.775 18.055 2434 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.29 % Allowed : 20.48 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 2229 helix: 2.69 (0.15), residues: 1349 sheet: -0.63 (0.42), residues: 170 loop : -0.91 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 671 HIS 0.008 0.001 HIS D 435 PHE 0.011 0.001 PHE G 73 TYR 0.016 0.001 TYR F 181 ARG 0.005 0.001 ARG G 6 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 1108) hydrogen bonds : angle 3.94726 ( 3282) SS BOND : bond 0.00381 ( 12) SS BOND : angle 1.05310 ( 24) covalent geometry : bond 0.00380 (17422) covalent geometry : angle 0.61794 (23660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.7033 (ttm) cc_final: 0.6056 (tmm) REVERT: A 674 MET cc_start: 0.6284 (mtm) cc_final: 0.5728 (mtt) REVERT: B 496 MET cc_start: 0.2875 (ppp) cc_final: 0.2610 (ppp) REVERT: B 503 MET cc_start: 0.7414 (tmm) cc_final: 0.6917 (tmm) REVERT: B 570 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8525 (mp0) REVERT: B 671 TRP cc_start: 0.7185 (t-100) cc_final: 0.6939 (t-100) REVERT: B 673 TYR cc_start: 0.7690 (t80) cc_final: 0.7350 (t80) REVERT: B 684 ARG cc_start: 0.4600 (tmt170) cc_final: 0.4348 (tmt170) REVERT: C 708 MET cc_start: 0.9040 (mtm) cc_final: 0.8534 (mpp) REVERT: D 407 MET cc_start: 0.8841 (mmm) cc_final: 0.8475 (mmm) REVERT: D 408 MET cc_start: 0.8915 (mmm) cc_final: 0.8295 (tpt) REVERT: D 424 TYR cc_start: 0.8236 (t80) cc_final: 0.7622 (m-80) REVERT: D 590 ASP cc_start: 0.8615 (t70) cc_final: 0.8283 (t0) REVERT: D 730 LYS cc_start: 0.6908 (mtmt) cc_final: 0.6557 (pttm) REVERT: E 10 MET cc_start: 0.8414 (mmm) cc_final: 0.7882 (tpt) REVERT: E 78 LYS cc_start: 0.8936 (pttt) cc_final: 0.8568 (pttm) REVERT: E 160 ASN cc_start: 0.8719 (m-40) cc_final: 0.8446 (t0) REVERT: E 176 TYR cc_start: 0.8996 (m-80) cc_final: 0.8507 (m-80) REVERT: F 61 SER cc_start: 0.9474 (t) cc_final: 0.9229 (p) REVERT: F 160 ASN cc_start: 0.8624 (m-40) cc_final: 0.8100 (m110) REVERT: F 192 MET cc_start: 0.8712 (mtt) cc_final: 0.8364 (mmp) REVERT: F 207 GLN cc_start: 0.9165 (tt0) cc_final: 0.8826 (tm-30) REVERT: G 10 MET cc_start: 0.8905 (mmm) cc_final: 0.8463 (tpp) REVERT: G 25 THR cc_start: 0.9562 (t) cc_final: 0.9326 (p) REVERT: G 81 ASP cc_start: 0.8420 (t0) cc_final: 0.8181 (t0) REVERT: G 99 ARG cc_start: 0.8774 (mtt-85) cc_final: 0.8155 (mtm-85) REVERT: H 31 ASP cc_start: 0.8395 (m-30) cc_final: 0.8153 (m-30) REVERT: H 35 TYR cc_start: 0.8387 (m-80) cc_final: 0.7733 (m-80) outliers start: 55 outliers final: 45 residues processed: 269 average time/residue: 0.3221 time to fit residues: 130.5115 Evaluate side-chains 267 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 688 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 15 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.131149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.079697 restraints weight = 67503.381| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 5.43 r_work: 0.2908 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17434 Z= 0.168 Angle : 0.631 12.751 23684 Z= 0.317 Chirality : 0.040 0.272 2745 Planarity : 0.004 0.055 2906 Dihedral : 3.765 17.975 2434 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.17 % Allowed : 21.02 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 2229 helix: 2.67 (0.15), residues: 1349 sheet: -0.70 (0.42), residues: 171 loop : -0.86 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 671 HIS 0.006 0.001 HIS E 82 PHE 0.012 0.001 PHE G 73 TYR 0.018 0.001 TYR F 181 ARG 0.006 0.001 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 1108) hydrogen bonds : angle 3.93489 ( 3282) SS BOND : bond 0.00381 ( 12) SS BOND : angle 1.08415 ( 24) covalent geometry : bond 0.00387 (17422) covalent geometry : angle 0.62999 (23660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.7081 (ttm) cc_final: 0.6791 (ttp) REVERT: A 674 MET cc_start: 0.6279 (mtm) cc_final: 0.5900 (mtt) REVERT: B 496 MET cc_start: 0.2705 (ppp) cc_final: 0.2474 (ppp) REVERT: B 503 MET cc_start: 0.7625 (tmm) cc_final: 0.7088 (tmm) REVERT: B 668 ASP cc_start: 0.8537 (m-30) cc_final: 0.8242 (p0) REVERT: B 673 TYR cc_start: 0.8070 (t80) cc_final: 0.7859 (t80) REVERT: B 684 ARG cc_start: 0.4407 (tmt170) cc_final: 0.4105 (tmt170) REVERT: C 708 MET cc_start: 0.9138 (mtm) cc_final: 0.8553 (mpp) REVERT: D 407 MET cc_start: 0.8805 (mmm) cc_final: 0.8434 (mmm) REVERT: D 408 MET cc_start: 0.8879 (mmm) cc_final: 0.8277 (tpt) REVERT: D 424 TYR cc_start: 0.8197 (t80) cc_final: 0.7565 (m-80) REVERT: D 590 ASP cc_start: 0.8636 (t70) cc_final: 0.8327 (t0) REVERT: D 671 TRP cc_start: 0.8093 (t-100) cc_final: 0.7854 (t-100) REVERT: E 10 MET cc_start: 0.8420 (mmm) cc_final: 0.7887 (tpt) REVERT: E 78 LYS cc_start: 0.8894 (pttt) cc_final: 0.8547 (pttm) REVERT: E 160 ASN cc_start: 0.8760 (m-40) cc_final: 0.8437 (t0) REVERT: F 28 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.9231 (p) REVERT: F 61 SER cc_start: 0.9470 (t) cc_final: 0.9217 (p) REVERT: F 160 ASN cc_start: 0.8507 (m-40) cc_final: 0.8062 (m110) REVERT: F 192 MET cc_start: 0.8750 (mtt) cc_final: 0.8398 (mmp) REVERT: F 207 GLN cc_start: 0.9188 (tt0) cc_final: 0.8836 (tm-30) REVERT: G 10 MET cc_start: 0.8940 (mmm) cc_final: 0.8520 (tpp) REVERT: G 25 THR cc_start: 0.9567 (t) cc_final: 0.9331 (p) REVERT: G 81 ASP cc_start: 0.8401 (t0) cc_final: 0.8158 (t0) REVERT: G 99 ARG cc_start: 0.8795 (mtt-85) cc_final: 0.8140 (mtm180) REVERT: H 6 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7959 (ptm-80) REVERT: H 31 ASP cc_start: 0.8374 (m-30) cc_final: 0.8154 (m-30) outliers start: 53 outliers final: 49 residues processed: 261 average time/residue: 0.3081 time to fit residues: 120.2980 Evaluate side-chains 270 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 199 optimal weight: 0.7980 chunk 43 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 204 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.133079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081699 restraints weight = 74076.942| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.69 r_work: 0.2965 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17434 Z= 0.120 Angle : 0.623 13.240 23684 Z= 0.310 Chirality : 0.040 0.276 2745 Planarity : 0.003 0.055 2906 Dihedral : 3.709 17.164 2434 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.51 % Allowed : 21.68 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 2229 helix: 2.74 (0.15), residues: 1350 sheet: -0.86 (0.42), residues: 170 loop : -0.80 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 671 HIS 0.005 0.001 HIS D 435 PHE 0.016 0.001 PHE B 682 TYR 0.013 0.001 TYR D 702 ARG 0.005 0.000 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1108) hydrogen bonds : angle 3.77095 ( 3282) SS BOND : bond 0.00336 ( 12) SS BOND : angle 0.97542 ( 24) covalent geometry : bond 0.00268 (17422) covalent geometry : angle 0.62275 (23660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.6873 (ttm) cc_final: 0.6578 (ttp) REVERT: A 587 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8365 (mm-40) REVERT: A 674 MET cc_start: 0.6138 (mtm) cc_final: 0.5791 (mtt) REVERT: A 748 LEU cc_start: 0.9241 (pp) cc_final: 0.8893 (mm) REVERT: B 496 MET cc_start: 0.2998 (ppp) cc_final: 0.2791 (ppp) REVERT: B 503 MET cc_start: 0.7769 (tmm) cc_final: 0.7209 (tmm) REVERT: B 668 ASP cc_start: 0.8601 (m-30) cc_final: 0.8370 (p0) REVERT: B 684 ARG cc_start: 0.4333 (tmt170) cc_final: 0.4005 (tmt170) REVERT: D 407 MET cc_start: 0.8767 (mmm) cc_final: 0.8447 (mmm) REVERT: D 408 MET cc_start: 0.8866 (mmm) cc_final: 0.8239 (tpt) REVERT: D 424 TYR cc_start: 0.8213 (t80) cc_final: 0.7535 (m-80) REVERT: D 590 ASP cc_start: 0.8590 (t70) cc_final: 0.8303 (t0) REVERT: D 671 TRP cc_start: 0.8089 (t-100) cc_final: 0.7856 (t-100) REVERT: D 730 LYS cc_start: 0.6881 (mtmt) cc_final: 0.6680 (pttm) REVERT: E 10 MET cc_start: 0.8358 (mmm) cc_final: 0.7928 (tpt) REVERT: E 160 ASN cc_start: 0.8772 (m-40) cc_final: 0.8376 (t0) REVERT: F 28 VAL cc_start: 0.9423 (OUTLIER) cc_final: 0.9175 (p) REVERT: F 61 SER cc_start: 0.9435 (t) cc_final: 0.9153 (p) REVERT: F 185 LEU cc_start: 0.9240 (tp) cc_final: 0.8984 (tp) REVERT: F 192 MET cc_start: 0.8698 (mtt) cc_final: 0.8317 (mmp) REVERT: F 207 GLN cc_start: 0.9140 (tt0) cc_final: 0.8779 (tm-30) REVERT: G 10 MET cc_start: 0.8923 (mmm) cc_final: 0.8471 (tpp) REVERT: G 25 THR cc_start: 0.9525 (t) cc_final: 0.9284 (p) REVERT: G 81 ASP cc_start: 0.8407 (t0) cc_final: 0.8183 (t0) REVERT: G 99 ARG cc_start: 0.8754 (mtt-85) cc_final: 0.8095 (mtm180) REVERT: G 110 LEU cc_start: 0.9337 (tp) cc_final: 0.8980 (tp) REVERT: G 206 LYS cc_start: 0.9655 (ttpt) cc_final: 0.9274 (tppt) REVERT: H 6 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7988 (ptm-80) REVERT: H 31 ASP cc_start: 0.8416 (m-30) cc_final: 0.8178 (m-30) outliers start: 42 outliers final: 34 residues processed: 269 average time/residue: 0.2985 time to fit residues: 119.5315 Evaluate side-chains 261 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 39 optimal weight: 30.0000 chunk 213 optimal weight: 6.9990 chunk 118 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 619 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.132724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081227 restraints weight = 80190.258| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 5.57 r_work: 0.2932 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17434 Z= 0.128 Angle : 0.632 12.470 23684 Z= 0.315 Chirality : 0.040 0.286 2745 Planarity : 0.004 0.057 2906 Dihedral : 3.697 17.232 2434 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.57 % Allowed : 21.86 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 2229 helix: 2.73 (0.15), residues: 1350 sheet: -0.64 (0.44), residues: 158 loop : -0.78 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 671 HIS 0.005 0.001 HIS D 435 PHE 0.022 0.001 PHE B 682 TYR 0.013 0.001 TYR C 523 ARG 0.005 0.000 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1108) hydrogen bonds : angle 3.79058 ( 3282) SS BOND : bond 0.00332 ( 12) SS BOND : angle 0.97203 ( 24) covalent geometry : bond 0.00292 (17422) covalent geometry : angle 0.63114 (23660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12112.17 seconds wall clock time: 212 minutes 0.32 seconds (12720.32 seconds total)