Starting phenix.real_space_refine on Sun Aug 24 04:35:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3x_17398/08_2025/8p3x_17398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3x_17398/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p3x_17398/08_2025/8p3x_17398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3x_17398/08_2025/8p3x_17398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p3x_17398/08_2025/8p3x_17398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3x_17398/08_2025/8p3x_17398.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 12, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1} 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: {'GLU:plan': 12, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1} 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: {'GLU:plan': 15, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 1} 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: {'GLU:plan': 13, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 5, 'ARG:plan': 6, 'GLN:plan1': 2, 'TYR:plan': 1} 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: {'GLU:plan': 13, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 1} 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: {'GLU:plan': 13, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 1} 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: {'ARG:plan': 2, 'GLU:plan': 1} 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: 6.24, per 1000 atoms: 0.37 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: 1.88 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.48 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: 3.06 Time building geometry restraints manager: 2.51 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.460 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG A 694 TYR 0.041 0.004 TYR A 647 PHE 0.032 0.004 PHE A 667 TRP 0.023 0.005 TRP A 767 HIS 0.009 0.002 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.01303 (17422) covalent geometry : angle 1.65641 (23660) SS BOND : bond 0.01615 ( 12) SS BOND : angle 2.24462 ( 24) hydrogen bonds : bond 0.15394 ( 1108) hydrogen bonds : angle 5.88658 ( 3282) *********************** 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 : 0.591 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: A 590 ASP cc_start: 0.8956 (p0) cc_final: 0.8646 (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: 0.4778 (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: -0.0890 (pt) REVERT: D 519 ASP cc_start: 0.9464 (m-30) cc_final: 0.9203 (m-30) REVERT: D 569 ASN cc_start: 0.7274 (m110) cc_final: 0.7013 (m-40) REVERT: E 78 LYS cc_start: 0.9264 (pttt) cc_final: 0.8879 (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: 0.8581 (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: 0.9077 (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: 0.8425 (tpp) REVERT: G 99 ARG cc_start: 0.9318 (mtt-85) cc_final: 0.8795 (mtm-85) REVERT: H 58 MET cc_start: 0.9375 (mmp) cc_final: 0.9127 (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: 0.1672 time to fit residues: 100.2677 Evaluate side-chains 245 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 237 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.134448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082172 restraints weight = 74234.323| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.99 r_work: 0.2969 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17434 Z= 0.158 Angle : 0.628 11.560 23684 Z= 0.337 Chirality : 0.043 0.272 2745 Planarity : 0.004 0.041 2906 Dihedral : 4.705 56.525 2451 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.34 % Allowed : 15.03 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.18), residues: 2229 helix: 2.02 (0.14), residues: 1325 sheet: -1.61 (0.37), residues: 162 loop : -1.50 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 594 TYR 0.017 0.001 TYR D 469 PHE 0.015 0.001 PHE D 623 TRP 0.022 0.001 TRP D 671 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00349 (17422) covalent geometry : angle 0.62719 (23660) SS BOND : bond 0.00340 ( 12) SS BOND : angle 1.40536 ( 24) hydrogen bonds : bond 0.04893 ( 1108) hydrogen bonds : angle 4.17043 ( 3282) *********************** 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 324 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 0.527 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: 0.6525 (ttm) cc_final: 0.6238 (ttp) REVERT: A 594 ARG cc_start: 0.9199 (mtm-85) cc_final: 0.8904 (mtp85) REVERT: A 674 MET cc_start: 0.6565 (mtm) cc_final: 0.5883 (mtt) REVERT: B 673 TYR cc_start: 0.7747 (t80) cc_final: 0.7457 (t80) REVERT: B 684 ARG cc_start: 0.4605 (tmt170) cc_final: 0.3993 (tmt170) REVERT: B 692 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8275 (ptm160) REVERT: B 721 MET cc_start: 0.5278 (ptt) cc_final: 0.4834 (ptp) REVERT: C 587 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8916 (tp-100) REVERT: C 708 MET cc_start: 0.8830 (mmt) cc_final: 0.8617 (mtt) REVERT: C 813 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8982 (tm-30) REVERT: D 407 MET cc_start: 0.9147 (tpp) cc_final: 0.8743 (mtm) REVERT: D 408 MET cc_start: 0.8694 (mmm) cc_final: 0.8451 (mmm) REVERT: D 424 TYR cc_start: 0.8245 (t80) cc_final: 0.7993 (t80) REVERT: D 519 ASP cc_start: 0.9125 (m-30) cc_final: 0.8813 (m-30) REVERT: D 590 ASP cc_start: 0.8800 (t70) cc_final: 0.8531 (t0) REVERT: E 37 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8538 (ttp80) REVERT: E 58 MET cc_start: 0.8925 (mmp) cc_final: 0.8350 (mmp) REVERT: E 70 GLU cc_start: 0.7763 (pp20) cc_final: 0.7548 (pp20) REVERT: E 78 LYS cc_start: 0.9111 (pttt) cc_final: 0.8606 (pttm) REVERT: E 192 MET cc_start: 0.8833 (mtt) cc_final: 0.8617 (mmt) REVERT: E 195 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.8999 (t) REVERT: F 24 MET cc_start: 0.9364 (tpt) cc_final: 0.9104 (tpt) REVERT: F 58 MET cc_start: 0.9198 (tpp) cc_final: 0.8699 (mmp) REVERT: F 99 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8480 (mmm-85) REVERT: F 110 LEU cc_start: 0.8908 (tp) cc_final: 0.8636 (tp) REVERT: F 160 ASN cc_start: 0.8623 (m-40) cc_final: 0.8240 (m110) REVERT: F 174 TYR cc_start: 0.8215 (p90) cc_final: 0.6992 (p90) REVERT: F 185 LEU cc_start: 0.9251 (tp) cc_final: 0.9020 (tp) REVERT: F 192 MET cc_start: 0.8669 (mtt) cc_final: 0.8306 (mmp) REVERT: F 207 GLN cc_start: 0.9254 (tt0) cc_final: 0.8821 (tm-30) REVERT: G 56 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8861 (mm-30) REVERT: G 81 ASP cc_start: 0.8339 (t0) cc_final: 0.8029 (t0) REVERT: G 99 ARG cc_start: 0.8804 (mtt-85) cc_final: 0.8219 (mtm-85) REVERT: H 31 ASP cc_start: 0.8473 (m-30) cc_final: 0.8110 (m-30) REVERT: H 41 LYS cc_start: 0.8538 (tppt) cc_final: 0.8332 (tppt) REVERT: H 42 THR cc_start: 0.8023 (p) cc_final: 0.7643 (p) outliers start: 39 outliers final: 18 residues processed: 310 average time/residue: 0.1347 time to fit residues: 61.8201 Evaluate side-chains 249 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 151 ILE 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 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 195 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 57 VAL 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 220 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 587 GLN B 619 ASN D 569 ASN E 9 GLN E 72 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.130729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078835 restraints weight = 96884.051| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 6.76 r_work: 0.2828 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17434 Z= 0.241 Angle : 0.643 10.794 23684 Z= 0.343 Chirality : 0.043 0.240 2745 Planarity : 0.004 0.039 2906 Dihedral : 4.177 51.918 2436 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.71 % Allowed : 15.69 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.19), residues: 2229 helix: 2.48 (0.15), residues: 1331 sheet: -1.30 (0.38), residues: 168 loop : -1.30 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 586 TYR 0.016 0.002 TYR D 732 PHE 0.016 0.002 PHE D 541 TRP 0.017 0.002 TRP A 766 HIS 0.008 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00553 (17422) covalent geometry : angle 0.64148 (23660) SS BOND : bond 0.00422 ( 12) SS BOND : angle 1.40231 ( 24) hydrogen bonds : bond 0.05034 ( 1108) hydrogen bonds : angle 4.26133 ( 3282) *********************** 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 293 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 0.672 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: 0.6996 (ttm) cc_final: 0.6040 (tmm) REVERT: A 594 ARG cc_start: 0.9357 (mtm-85) cc_final: 0.9053 (mtp85) REVERT: A 674 MET cc_start: 0.6623 (mtm) cc_final: 0.5965 (mtt) REVERT: B 496 MET cc_start: 0.3728 (ttp) cc_final: 0.3471 (ppp) REVERT: B 503 MET cc_start: 0.7145 (tmm) cc_final: 0.6861 (tmm) REVERT: B 570 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8448 (mp0) REVERT: B 673 TYR cc_start: 0.7827 (t80) cc_final: 0.7622 (t80) REVERT: B 674 MET cc_start: 0.8107 (tpp) cc_final: 0.7790 (tpp) REVERT: B 684 ARG cc_start: 0.4787 (tmt170) cc_final: 0.4444 (tmt170) REVERT: B 721 MET cc_start: 0.5564 (ptt) cc_final: 0.5279 (ptp) REVERT: C 708 MET cc_start: 0.8738 (mmt) cc_final: 0.8389 (mtm) REVERT: C 813 GLU cc_start: 0.9350 (tm-30) cc_final: 0.9079 (tm-30) REVERT: D 424 TYR cc_start: 0.8310 (t80) cc_final: 0.7939 (t80) REVERT: D 503 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6543 (mmp) REVERT: D 519 ASP cc_start: 0.9222 (m-30) cc_final: 0.8861 (m-30) REVERT: D 524 GLU cc_start: 0.9206 (mp0) cc_final: 0.8967 (mp0) REVERT: D 590 ASP cc_start: 0.8842 (t70) cc_final: 0.8509 (t0) REVERT: E 58 MET cc_start: 0.9059 (mmp) cc_final: 0.8796 (mmp) REVERT: E 78 LYS cc_start: 0.9057 (pttt) cc_final: 0.8599 (pttm) REVERT: E 160 ASN cc_start: 0.8606 (t0) cc_final: 0.8264 (t0) REVERT: F 95 GLU cc_start: 0.8349 (pp20) cc_final: 0.8040 (pp20) REVERT: F 99 ARG cc_start: 0.8829 (tpp80) cc_final: 0.8548 (mtm180) REVERT: F 126 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8779 (mm-30) REVERT: F 174 TYR cc_start: 0.8624 (p90) cc_final: 0.8420 (p90) REVERT: F 192 MET cc_start: 0.8839 (mtt) cc_final: 0.8494 (mmp) REVERT: F 207 GLN cc_start: 0.9238 (tt0) cc_final: 0.8834 (tm-30) REVERT: G 81 ASP cc_start: 0.8442 (t0) cc_final: 0.8149 (t0) REVERT: G 99 ARG cc_start: 0.8882 (mtt-85) cc_final: 0.8323 (mtm180) REVERT: G 117 MET cc_start: 0.9185 (mmp) cc_final: 0.8901 (mmp) REVERT: H 31 ASP cc_start: 0.8460 (m-30) cc_final: 0.8098 (m-30) REVERT: H 35 TYR cc_start: 0.8333 (m-80) cc_final: 0.7859 (m-80) REVERT: H 41 LYS cc_start: 0.8562 (tppt) cc_final: 0.8132 (tppt) REVERT: H 42 THR cc_start: 0.7976 (p) cc_final: 0.7703 (p) REVERT: H 76 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6503 (tp) outliers start: 62 outliers final: 36 residues processed: 278 average time/residue: 0.1535 time to fit residues: 62.9677 Evaluate side-chains 253 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 VAL 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 570 GLU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 500 ILE 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 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 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL 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 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 61 SER Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 0.0000 chunk 199 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 217 optimal weight: 0.0050 chunk 204 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 39 optimal weight: 40.0000 chunk 77 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 F 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.134281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079260 restraints weight = 62539.157| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.04 r_work: 0.3011 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17434 Z= 0.116 Angle : 0.580 11.647 23684 Z= 0.299 Chirality : 0.040 0.222 2745 Planarity : 0.003 0.041 2906 Dihedral : 3.951 38.676 2436 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.57 % Allowed : 17.13 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.19), residues: 2229 helix: 2.71 (0.15), residues: 1336 sheet: -0.84 (0.41), residues: 162 loop : -1.18 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 453 TYR 0.012 0.001 TYR D 732 PHE 0.020 0.001 PHE E 127 TRP 0.017 0.001 TRP D 671 HIS 0.027 0.001 HIS G 205 Details of bonding type rmsd covalent geometry : bond 0.00249 (17422) covalent geometry : angle 0.57879 (23660) SS BOND : bond 0.00393 ( 12) SS BOND : angle 1.12900 ( 24) hydrogen bonds : bond 0.03842 ( 1108) hydrogen bonds : angle 3.87638 ( 3282) *********************** 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 301 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.6562 (ttm) cc_final: 0.5633 (tmm) REVERT: A 497 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7851 (t) REVERT: A 674 MET cc_start: 0.6497 (mtm) cc_final: 0.5825 (mtt) REVERT: B 431 GLU cc_start: 0.7065 (pm20) cc_final: 0.6843 (pm20) REVERT: B 503 MET cc_start: 0.7310 (tmm) cc_final: 0.6969 (tmm) REVERT: B 673 TYR cc_start: 0.7916 (t80) cc_final: 0.7586 (t80) REVERT: B 674 MET cc_start: 0.8063 (tpp) cc_final: 0.7769 (tpp) REVERT: B 684 ARG cc_start: 0.4646 (tmt170) cc_final: 0.4282 (tmt170) REVERT: B 721 MET cc_start: 0.5421 (ptt) cc_final: 0.5171 (ptp) REVERT: C 708 MET cc_start: 0.8786 (mmt) cc_final: 0.8444 (mtm) REVERT: C 811 LEU cc_start: 0.9351 (mt) cc_final: 0.9111 (mm) REVERT: D 407 MET cc_start: 0.8495 (mmm) cc_final: 0.8182 (mmm) REVERT: D 408 MET cc_start: 0.8845 (mmm) cc_final: 0.7972 (tpt) REVERT: D 424 TYR cc_start: 0.8209 (t80) cc_final: 0.7901 (t80) REVERT: D 503 MET cc_start: 0.7549 (tpp) cc_final: 0.6811 (mmp) REVERT: D 519 ASP cc_start: 0.9131 (m-30) cc_final: 0.8704 (m-30) REVERT: D 524 GLU cc_start: 0.8816 (mp0) cc_final: 0.8549 (mp0) REVERT: D 590 ASP cc_start: 0.8630 (t70) cc_final: 0.8279 (t0) REVERT: D 688 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8246 (pt0) REVERT: E 10 MET cc_start: 0.8507 (mmm) cc_final: 0.8107 (tpt) REVERT: E 58 MET cc_start: 0.8957 (mmp) cc_final: 0.8566 (mmp) REVERT: E 78 LYS cc_start: 0.8980 (pttt) cc_final: 0.8515 (pttm) REVERT: E 151 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9268 (tt) REVERT: E 160 ASN cc_start: 0.8608 (t0) cc_final: 0.8315 (t0) REVERT: E 176 TYR cc_start: 0.8820 (m-80) cc_final: 0.8222 (m-80) REVERT: E 203 ASP cc_start: 0.8939 (m-30) cc_final: 0.8476 (m-30) REVERT: F 24 MET cc_start: 0.9368 (tpt) cc_final: 0.9076 (tpt) REVERT: F 81 ASP cc_start: 0.8874 (t0) cc_final: 0.8553 (t0) REVERT: F 95 GLU cc_start: 0.7946 (pp20) cc_final: 0.7709 (pp20) REVERT: F 99 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8370 (mtm180) REVERT: F 110 LEU cc_start: 0.8891 (tp) cc_final: 0.8546 (tp) REVERT: F 185 LEU cc_start: 0.9198 (tp) cc_final: 0.8938 (tp) REVERT: F 192 MET cc_start: 0.8622 (mtt) cc_final: 0.8299 (mmp) REVERT: F 207 GLN cc_start: 0.9086 (tt0) cc_final: 0.8713 (tm-30) REVERT: G 81 ASP cc_start: 0.8392 (t0) cc_final: 0.8129 (t0) REVERT: G 99 ARG cc_start: 0.8730 (mtt-85) cc_final: 0.8153 (mtm180) REVERT: H 31 ASP cc_start: 0.8226 (m-30) cc_final: 0.7955 (m-30) REVERT: H 35 TYR cc_start: 0.8150 (m-80) cc_final: 0.7904 (m-80) REVERT: H 41 LYS cc_start: 0.8666 (tppt) cc_final: 0.8252 (tppt) REVERT: H 42 THR cc_start: 0.7954 (p) cc_final: 0.7677 (p) outliers start: 43 outliers final: 22 residues processed: 290 average time/residue: 0.1436 time to fit residues: 61.5481 Evaluate side-chains 252 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 587 GLN 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 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE 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 151 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain H residue 117 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 57 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 39 optimal weight: 40.0000 chunk 153 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 109 optimal weight: 40.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 587 GLN B 619 ASN D 791 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS H 149 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.131416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.079301 restraints weight = 62185.534| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 5.28 r_work: 0.2897 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17434 Z= 0.196 Angle : 0.620 11.382 23684 Z= 0.321 Chirality : 0.041 0.222 2745 Planarity : 0.004 0.043 2906 Dihedral : 3.864 31.284 2435 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.59 % Allowed : 18.50 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.19), residues: 2229 helix: 2.73 (0.15), residues: 1333 sheet: -0.85 (0.41), residues: 168 loop : -1.11 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 453 TYR 0.016 0.001 TYR F 181 PHE 0.017 0.002 PHE E 127 TRP 0.016 0.001 TRP B 671 HIS 0.006 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00454 (17422) covalent geometry : angle 0.61883 (23660) SS BOND : bond 0.00442 ( 12) SS BOND : angle 1.39745 ( 24) hydrogen bonds : bond 0.04444 ( 1108) hydrogen bonds : angle 4.03476 ( 3282) *********************** 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 293 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 0.665 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: 0.6822 (ttm) cc_final: 0.5978 (tmm) REVERT: A 497 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7927 (t) REVERT: A 503 MET cc_start: 0.8084 (ppp) cc_final: 0.7880 (ppp) REVERT: A 627 GLU cc_start: 0.7939 (mp0) cc_final: 0.7404 (mp0) REVERT: A 674 MET cc_start: 0.6510 (mtm) cc_final: 0.5857 (mtt) REVERT: B 503 MET cc_start: 0.7406 (tmm) cc_final: 0.6752 (tmm) REVERT: B 570 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8479 (mp0) REVERT: B 673 TYR cc_start: 0.7942 (t80) cc_final: 0.7588 (t80) REVERT: B 674 MET cc_start: 0.8238 (tpp) cc_final: 0.7954 (tpp) REVERT: B 684 ARG cc_start: 0.4773 (tmt170) cc_final: 0.4339 (tmt170) REVERT: C 708 MET cc_start: 0.8797 (mmt) cc_final: 0.8365 (mtm) REVERT: C 811 LEU cc_start: 0.9415 (mt) cc_final: 0.9185 (mm) REVERT: D 407 MET cc_start: 0.8945 (mmm) cc_final: 0.8648 (mmm) REVERT: D 408 MET cc_start: 0.8901 (mmm) cc_final: 0.8061 (tpt) REVERT: D 424 TYR cc_start: 0.8191 (t80) cc_final: 0.7913 (t80) REVERT: D 503 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6903 (mmp) REVERT: D 519 ASP cc_start: 0.9285 (m-30) cc_final: 0.9029 (m-30) REVERT: D 524 GLU cc_start: 0.9025 (mp0) cc_final: 0.8805 (mp0) REVERT: D 590 ASP cc_start: 0.8728 (t70) cc_final: 0.8375 (t0) REVERT: D 688 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8258 (pt0) REVERT: E 10 MET cc_start: 0.8599 (mmm) cc_final: 0.8226 (tpt) REVERT: E 78 LYS cc_start: 0.8978 (pttt) cc_final: 0.8606 (pttm) REVERT: E 160 ASN cc_start: 0.8739 (t0) cc_final: 0.8360 (t0) REVERT: E 176 TYR cc_start: 0.8993 (m-80) cc_final: 0.8456 (m-80) REVERT: F 58 MET cc_start: 0.9245 (tpp) cc_final: 0.8687 (mmp) REVERT: F 81 ASP cc_start: 0.8873 (t0) cc_final: 0.8568 (t0) REVERT: F 192 MET cc_start: 0.8681 (mtt) cc_final: 0.8339 (mmp) REVERT: F 207 GLN cc_start: 0.9174 (tt0) cc_final: 0.8779 (tm-30) REVERT: G 10 MET cc_start: 0.8787 (mmm) cc_final: 0.8284 (tpp) REVERT: G 14 THR cc_start: 0.9380 (t) cc_final: 0.9038 (p) REVERT: G 58 MET cc_start: 0.7907 (tpp) cc_final: 0.7511 (mmm) REVERT: G 81 ASP cc_start: 0.8461 (t0) cc_final: 0.8184 (t0) REVERT: G 99 ARG cc_start: 0.8870 (mtt-85) cc_final: 0.8302 (mtm180) REVERT: H 24 MET cc_start: 0.9266 (tpt) cc_final: 0.8974 (tpp) REVERT: H 35 TYR cc_start: 0.8306 (m-80) cc_final: 0.7574 (m-80) REVERT: H 41 LYS cc_start: 0.8619 (tppt) cc_final: 0.8140 (tppt) REVERT: H 42 THR cc_start: 0.7967 (p) cc_final: 0.7709 (p) REVERT: H 200 MET cc_start: 0.9184 (mtm) cc_final: 0.8653 (tpt) outliers start: 60 outliers final: 40 residues processed: 276 average time/residue: 0.1555 time to fit residues: 62.6044 Evaluate side-chains 267 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 412 HIS Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 811 LEU 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 503 MET Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU 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 153 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 26 ILE 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 61 SER Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 221 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN F 205 HIS ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.132770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080230 restraints weight = 69360.121| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 5.58 r_work: 0.2915 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 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 = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17434 Z= 0.141 Angle : 0.582 11.292 23684 Z= 0.300 Chirality : 0.040 0.219 2745 Planarity : 0.003 0.046 2906 Dihedral : 3.775 21.977 2435 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.29 % Allowed : 18.68 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.19), residues: 2229 helix: 2.80 (0.15), residues: 1335 sheet: -0.87 (0.40), residues: 173 loop : -1.06 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 37 TYR 0.018 0.001 TYR F 156 PHE 0.016 0.001 PHE G 73 TRP 0.018 0.001 TRP D 671 HIS 0.005 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00320 (17422) covalent geometry : angle 0.58079 (23660) SS BOND : bond 0.00353 ( 12) SS BOND : angle 1.21389 ( 24) hydrogen bonds : bond 0.04030 ( 1108) hydrogen bonds : angle 3.88929 ( 3282) *********************** 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 291 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 236 time to evaluate : 0.544 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: 0.6775 (ttm) cc_final: 0.5921 (tmm) REVERT: A 497 SER cc_start: 0.8250 (OUTLIER) cc_final: 0.7887 (t) REVERT: A 627 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: A 674 MET cc_start: 0.6408 (mtm) cc_final: 0.5737 (mtt) REVERT: B 408 MET cc_start: 0.8214 (tpt) cc_final: 0.7265 (tpt) REVERT: B 503 MET cc_start: 0.7488 (tmm) cc_final: 0.6779 (tmm) REVERT: B 570 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8505 (mp0) REVERT: B 673 TYR cc_start: 0.7927 (t80) cc_final: 0.7558 (t80) REVERT: B 674 MET cc_start: 0.8262 (tpp) cc_final: 0.7992 (tpp) REVERT: B 684 ARG cc_start: 0.4503 (tmt170) cc_final: 0.4139 (tmt170) REVERT: C 708 MET cc_start: 0.8772 (mmt) cc_final: 0.8356 (mtm) REVERT: C 811 LEU cc_start: 0.9428 (mt) cc_final: 0.9203 (mm) REVERT: D 407 MET cc_start: 0.9002 (mmm) cc_final: 0.8738 (mmt) REVERT: D 408 MET cc_start: 0.8794 (mmm) cc_final: 0.8566 (mmm) REVERT: D 424 TYR cc_start: 0.8236 (t80) cc_final: 0.7971 (t80) REVERT: D 503 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7091 (mmp) REVERT: D 519 ASP cc_start: 0.9301 (m-30) cc_final: 0.9031 (m-30) REVERT: D 524 GLU cc_start: 0.8959 (mp0) cc_final: 0.8720 (mp0) REVERT: D 590 ASP cc_start: 0.8715 (t70) cc_final: 0.8382 (t0) REVERT: E 10 MET cc_start: 0.8598 (mmm) cc_final: 0.8256 (tpt) REVERT: E 78 LYS cc_start: 0.8897 (pttt) cc_final: 0.8529 (pttm) REVERT: E 128 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: E 151 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9260 (tt) REVERT: E 160 ASN cc_start: 0.8704 (t0) cc_final: 0.8360 (t0) REVERT: E 176 TYR cc_start: 0.8960 (m-80) cc_final: 0.8396 (m-80) REVERT: F 58 MET cc_start: 0.9261 (tpp) cc_final: 0.8730 (mmp) REVERT: F 81 ASP cc_start: 0.9038 (t0) cc_final: 0.8815 (t0) REVERT: F 110 LEU cc_start: 0.8997 (tp) cc_final: 0.8599 (tp) REVERT: F 192 MET cc_start: 0.8710 (mtt) cc_final: 0.8359 (mmp) REVERT: F 207 GLN cc_start: 0.9149 (tt0) cc_final: 0.8779 (tm-30) REVERT: G 10 MET cc_start: 0.8690 (mmm) cc_final: 0.8163 (tpp) REVERT: G 14 THR cc_start: 0.9363 (t) cc_final: 0.9023 (p) REVERT: G 81 ASP cc_start: 0.8446 (t0) cc_final: 0.8205 (t0) REVERT: G 99 ARG cc_start: 0.8819 (mtt-85) cc_final: 0.8197 (mtm180) REVERT: H 35 TYR cc_start: 0.8254 (m-80) cc_final: 0.7599 (m-80) REVERT: H 41 LYS cc_start: 0.8708 (tppt) cc_final: 0.8187 (tppt) REVERT: H 42 THR cc_start: 0.7996 (p) cc_final: 0.7762 (p) REVERT: H 200 MET cc_start: 0.9182 (mtm) cc_final: 0.8581 (tpt) outliers start: 55 outliers final: 40 residues processed: 274 average time/residue: 0.1562 time to fit residues: 62.7502 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 : 0.692 ------------------------------------------------------------------------------- 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 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 627 GLU 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 B residue 811 LEU 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 464 VAL Chi-restraints excluded: chain D residue 503 MET 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 128 TYR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 26 ILE 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 155 VAL Chi-restraints excluded: chain F residue 195 VAL 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 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 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 37 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 119 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 118 optimal weight: 0.0040 chunk 102 optimal weight: 8.9990 overall best weight: 0.9974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN F 205 HIS H 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.133110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.077608 restraints weight = 62101.101| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.15 r_work: 0.2983 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17434 Z= 0.126 Angle : 0.586 11.664 23684 Z= 0.298 Chirality : 0.040 0.203 2745 Planarity : 0.004 0.049 2906 Dihedral : 3.696 17.229 2434 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.29 % Allowed : 19.40 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.19), residues: 2229 helix: 2.83 (0.15), residues: 1341 sheet: -0.79 (0.40), residues: 173 loop : -1.02 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 453 TYR 0.015 0.001 TYR D 702 PHE 0.015 0.001 PHE G 73 TRP 0.019 0.001 TRP D 671 HIS 0.005 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00283 (17422) covalent geometry : angle 0.58571 (23660) SS BOND : bond 0.00311 ( 12) SS BOND : angle 1.02939 ( 24) hydrogen bonds : bond 0.03836 ( 1108) hydrogen bonds : angle 3.82628 ( 3282) *********************** 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 295 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.649 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: 0.6652 (ttm) cc_final: 0.5737 (tmm) REVERT: A 497 SER cc_start: 0.8198 (OUTLIER) cc_final: 0.7831 (t) REVERT: A 627 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: A 674 MET cc_start: 0.6382 (mtm) cc_final: 0.5776 (mtt) REVERT: B 485 ARG cc_start: 0.3528 (mtt180) cc_final: 0.3120 (ptp-170) REVERT: B 503 MET cc_start: 0.7490 (tmm) cc_final: 0.6832 (tmm) REVERT: B 570 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8458 (mp0) REVERT: B 673 TYR cc_start: 0.7800 (t80) cc_final: 0.7431 (t80) REVERT: B 674 MET cc_start: 0.8246 (tpp) cc_final: 0.8032 (tpp) REVERT: B 684 ARG cc_start: 0.4550 (tmt170) cc_final: 0.4118 (tmt170) REVERT: B 692 ARG cc_start: 0.8599 (ttm110) cc_final: 0.8052 (ptp-170) REVERT: C 811 LEU cc_start: 0.9436 (mt) cc_final: 0.9231 (mm) REVERT: D 424 TYR cc_start: 0.8227 (t80) cc_final: 0.8025 (t80) REVERT: D 503 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7164 (mmp) REVERT: D 519 ASP cc_start: 0.9256 (m-30) cc_final: 0.8989 (m-30) REVERT: D 590 ASP cc_start: 0.8544 (t70) cc_final: 0.8218 (t0) REVERT: D 674 MET cc_start: 0.7056 (mmm) cc_final: 0.6813 (mmm) REVERT: E 10 MET cc_start: 0.8459 (mmm) cc_final: 0.8058 (tpt) REVERT: E 78 LYS cc_start: 0.8872 (pttt) cc_final: 0.8466 (pttm) REVERT: E 128 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: E 151 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9227 (tt) REVERT: E 160 ASN cc_start: 0.8691 (t0) cc_final: 0.8325 (t0) REVERT: F 110 LEU cc_start: 0.8970 (tp) cc_final: 0.8605 (tp) REVERT: F 185 LEU cc_start: 0.9292 (tp) cc_final: 0.9040 (tp) REVERT: F 192 MET cc_start: 0.8728 (mtt) cc_final: 0.8370 (mmp) REVERT: F 207 GLN cc_start: 0.9130 (tt0) cc_final: 0.8786 (tm-30) REVERT: G 10 MET cc_start: 0.8654 (mmm) cc_final: 0.8436 (tpp) REVERT: G 41 LYS cc_start: 0.8434 (tmtt) cc_final: 0.8212 (tptt) REVERT: G 81 ASP cc_start: 0.8424 (t0) cc_final: 0.8205 (t0) REVERT: G 99 ARG cc_start: 0.8730 (mtt-85) cc_final: 0.8064 (mtm-85) REVERT: H 41 LYS cc_start: 0.8691 (tppt) cc_final: 0.8156 (tppt) REVERT: H 200 MET cc_start: 0.9103 (mtm) cc_final: 0.8573 (tpt) REVERT: H 207 GLN cc_start: 0.8386 (pp30) cc_final: 0.8115 (pp30) outliers start: 55 outliers final: 39 residues processed: 281 average time/residue: 0.1406 time to fit residues: 58.6675 Evaluate side-chains 268 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 A residue 627 GLU 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 591 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 811 LEU 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 503 MET 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 128 TYR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 195 VAL 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 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 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 102 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 31 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 194 optimal weight: 0.0670 chunk 82 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS H 149 ASN H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.132720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082346 restraints weight = 65058.590| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 6.28 r_work: 0.2924 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 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 = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4789 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= 0.133 Angle : 0.605 12.417 23684 Z= 0.305 Chirality : 0.040 0.216 2745 Planarity : 0.003 0.050 2906 Dihedral : 3.672 17.109 2434 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.87 % Allowed : 20.78 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.19), residues: 2229 helix: 2.79 (0.14), residues: 1349 sheet: -0.68 (0.42), residues: 165 loop : -0.97 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 453 TYR 0.021 0.001 TYR F 156 PHE 0.014 0.001 PHE G 73 TRP 0.019 0.001 TRP D 671 HIS 0.007 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00301 (17422) covalent geometry : angle 0.60414 (23660) SS BOND : bond 0.00371 ( 12) SS BOND : angle 1.12119 ( 24) hydrogen bonds : bond 0.03845 ( 1108) hydrogen bonds : angle 3.82023 ( 3282) *********************** 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 280 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 0.540 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: 0.6769 (ttm) cc_final: 0.6488 (ttp) REVERT: A 627 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: A 674 MET cc_start: 0.6361 (mtm) cc_final: 0.5644 (mtt) REVERT: A 748 LEU cc_start: 0.9215 (pp) cc_final: 0.8903 (mm) REVERT: B 485 ARG cc_start: 0.3430 (mtt180) cc_final: 0.2977 (ptp-170) REVERT: B 503 MET cc_start: 0.7465 (tmm) cc_final: 0.6931 (tmm) REVERT: B 570 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8538 (mp0) REVERT: B 673 TYR cc_start: 0.7746 (t80) cc_final: 0.7400 (t80) REVERT: B 674 MET cc_start: 0.8336 (tpp) cc_final: 0.8077 (tpp) REVERT: B 684 ARG cc_start: 0.4554 (tmt170) cc_final: 0.4038 (tmt170) REVERT: C 811 LEU cc_start: 0.9455 (mt) cc_final: 0.9245 (mm) REVERT: D 407 MET cc_start: 0.7304 (mmm) cc_final: 0.6806 (mmm) REVERT: D 408 MET cc_start: 0.8609 (mmm) cc_final: 0.7603 (tpt) REVERT: D 424 TYR cc_start: 0.8255 (t80) cc_final: 0.8033 (t80) REVERT: D 503 MET cc_start: 0.7893 (tpp) cc_final: 0.7221 (mmp) REVERT: D 519 ASP cc_start: 0.9313 (m-30) cc_final: 0.9057 (m-30) REVERT: D 590 ASP cc_start: 0.8671 (t70) cc_final: 0.8374 (t0) REVERT: D 674 MET cc_start: 0.6912 (mmm) cc_final: 0.6603 (mmm) REVERT: E 10 MET cc_start: 0.8539 (mmm) cc_final: 0.8135 (tpt) REVERT: E 128 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: E 151 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9254 (tt) REVERT: E 160 ASN cc_start: 0.8680 (t0) cc_final: 0.8302 (t0) REVERT: F 110 LEU cc_start: 0.8968 (tp) cc_final: 0.8606 (tp) REVERT: F 126 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8855 (mm-30) REVERT: F 185 LEU cc_start: 0.9341 (tp) cc_final: 0.9107 (tp) REVERT: F 192 MET cc_start: 0.8774 (mtt) cc_final: 0.8400 (mmp) REVERT: F 207 GLN cc_start: 0.9140 (tt0) cc_final: 0.8773 (tm-30) REVERT: G 10 MET cc_start: 0.8720 (mmm) cc_final: 0.8438 (tpp) REVERT: G 41 LYS cc_start: 0.8398 (tmtt) cc_final: 0.8154 (tptt) REVERT: G 81 ASP cc_start: 0.8468 (t0) cc_final: 0.8248 (t0) REVERT: G 99 ARG cc_start: 0.8805 (mtt-85) cc_final: 0.8134 (mtm-85) REVERT: G 117 MET cc_start: 0.9292 (mmp) cc_final: 0.9089 (mmp) REVERT: H 6 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7958 (ptm-80) REVERT: H 78 LYS cc_start: 0.8885 (ptmt) cc_final: 0.8324 (pttm) REVERT: H 200 MET cc_start: 0.9198 (mtm) cc_final: 0.8657 (tpt) REVERT: H 207 GLN cc_start: 0.8662 (pp30) cc_final: 0.8395 (pp30) outliers start: 48 outliers final: 40 residues processed: 268 average time/residue: 0.1191 time to fit residues: 47.8170 Evaluate side-chains 268 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 627 GLU 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 B residue 811 LEU 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 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 128 TYR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 195 VAL 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 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 149 ASN Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 2 optimal weight: 0.0060 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 205 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 17 optimal weight: 0.0060 overall best weight: 0.9414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS F 205 HIS H 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081778 restraints weight = 88640.196| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 5.62 r_work: 0.2938 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 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 = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17434 Z= 0.124 Angle : 0.607 12.885 23684 Z= 0.304 Chirality : 0.039 0.216 2745 Planarity : 0.003 0.049 2906 Dihedral : 3.656 16.791 2434 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.99 % Allowed : 21.14 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.19), residues: 2229 helix: 2.84 (0.14), residues: 1347 sheet: -0.79 (0.43), residues: 155 loop : -0.93 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 453 TYR 0.018 0.001 TYR C 424 PHE 0.014 0.001 PHE G 73 TRP 0.022 0.001 TRP D 671 HIS 0.005 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00279 (17422) covalent geometry : angle 0.60645 (23660) SS BOND : bond 0.00297 ( 12) SS BOND : angle 1.04757 ( 24) hydrogen bonds : bond 0.03721 ( 1108) hydrogen bonds : angle 3.79081 ( 3282) *********************** 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 279 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.555 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 407 MET cc_start: 0.8419 (mpp) cc_final: 0.8165 (mpp) REVERT: A 496 MET cc_start: 0.6665 (ttm) cc_final: 0.5701 (tmm) REVERT: A 627 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: A 674 MET cc_start: 0.6233 (mtm) cc_final: 0.5565 (mtt) REVERT: A 748 LEU cc_start: 0.9229 (pp) cc_final: 0.8947 (mm) REVERT: B 503 MET cc_start: 0.7484 (tmm) cc_final: 0.6949 (tmm) REVERT: B 570 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8445 (mp0) REVERT: B 668 ASP cc_start: 0.8434 (m-30) cc_final: 0.7971 (p0) REVERT: B 673 TYR cc_start: 0.7772 (t80) cc_final: 0.7434 (t80) REVERT: B 674 MET cc_start: 0.8385 (tpp) cc_final: 0.8158 (tpp) REVERT: B 684 ARG cc_start: 0.4560 (tmt170) cc_final: 0.3996 (tmt170) REVERT: B 721 MET cc_start: 0.5199 (pmm) cc_final: 0.4932 (pmm) REVERT: D 407 MET cc_start: 0.7641 (mmm) cc_final: 0.7157 (mmm) REVERT: D 408 MET cc_start: 0.8702 (mmm) cc_final: 0.7732 (tpt) REVERT: D 424 TYR cc_start: 0.8382 (t80) cc_final: 0.8168 (t80) REVERT: D 519 ASP cc_start: 0.9233 (m-30) cc_final: 0.8814 (m-30) REVERT: D 590 ASP cc_start: 0.8679 (t70) cc_final: 0.8391 (t0) REVERT: D 730 LYS cc_start: 0.6995 (mtmt) cc_final: 0.6652 (pttm) REVERT: E 10 MET cc_start: 0.8527 (mmm) cc_final: 0.8135 (tpt) REVERT: E 128 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: E 151 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9236 (tt) REVERT: E 160 ASN cc_start: 0.8705 (t0) cc_final: 0.8338 (t0) REVERT: E 203 ASP cc_start: 0.9111 (m-30) cc_final: 0.8556 (m-30) REVERT: F 61 SER cc_start: 0.9412 (t) cc_final: 0.9186 (p) REVERT: F 110 LEU cc_start: 0.9042 (tp) cc_final: 0.8686 (tp) REVERT: F 126 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8889 (mm-30) REVERT: F 185 LEU cc_start: 0.9331 (tp) cc_final: 0.9106 (tp) REVERT: F 192 MET cc_start: 0.8769 (mtt) cc_final: 0.8382 (mmp) REVERT: F 207 GLN cc_start: 0.9143 (tt0) cc_final: 0.8774 (tm-30) REVERT: G 10 MET cc_start: 0.8728 (mmm) cc_final: 0.8430 (tpp) REVERT: G 41 LYS cc_start: 0.8328 (tmtt) cc_final: 0.8122 (tptt) REVERT: G 81 ASP cc_start: 0.8488 (t0) cc_final: 0.8275 (t0) REVERT: G 99 ARG cc_start: 0.8804 (mtt-85) cc_final: 0.8127 (mtm-85) REVERT: G 117 MET cc_start: 0.9337 (mmp) cc_final: 0.9124 (mmp) REVERT: H 6 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7824 (ptm-80) REVERT: H 200 MET cc_start: 0.9169 (mtm) cc_final: 0.8628 (tpt) REVERT: H 207 GLN cc_start: 0.8781 (pp30) cc_final: 0.8560 (pp30) outliers start: 50 outliers final: 41 residues processed: 269 average time/residue: 0.1245 time to fit residues: 50.0894 Evaluate side-chains 266 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 627 GLU 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 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 811 LEU 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 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 128 TYR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 117 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 195 VAL 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 G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER 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 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 139 optimal weight: 40.0000 chunk 209 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 220 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 122 optimal weight: 0.0570 chunk 88 optimal weight: 30.0000 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN E 205 HIS F 205 HIS H 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.132831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081531 restraints weight = 102270.127| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 6.55 r_work: 0.2901 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2901 ------------------------------------------------------------------------------- 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 = 0.43 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: 0.8303 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17434 Z= 0.136 Angle : 0.625 13.568 23684 Z= 0.314 Chirality : 0.040 0.248 2745 Planarity : 0.004 0.054 2906 Dihedral : 3.686 18.503 2434 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.99 % Allowed : 21.38 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.19), residues: 2229 helix: 2.79 (0.14), residues: 1347 sheet: -0.83 (0.43), residues: 160 loop : -0.89 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 453 TYR 0.016 0.001 TYR F 156 PHE 0.014 0.001 PHE G 73 TRP 0.062 0.001 TRP D 671 HIS 0.009 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00311 (17422) covalent geometry : angle 0.62449 (23660) SS BOND : bond 0.00296 ( 12) SS BOND : angle 1.01200 ( 24) hydrogen bonds : bond 0.03813 ( 1108) hydrogen bonds : angle 3.82422 ( 3282) ********************** 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 278 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.667 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: 0.6742 (ttm) cc_final: 0.5834 (tmm) REVERT: A 627 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: A 674 MET cc_start: 0.5987 (mtm) cc_final: 0.5636 (mtt) REVERT: A 748 LEU cc_start: 0.9221 (pp) cc_final: 0.8936 (mm) REVERT: B 503 MET cc_start: 0.7398 (tmm) cc_final: 0.6904 (tmm) REVERT: B 570 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8495 (mp0) REVERT: B 668 ASP cc_start: 0.8647 (m-30) cc_final: 0.8396 (p0) REVERT: B 671 TRP cc_start: 0.7094 (t-100) cc_final: 0.6785 (t-100) REVERT: B 673 TYR cc_start: 0.7771 (t80) cc_final: 0.7416 (t80) REVERT: B 684 ARG cc_start: 0.4570 (tmt170) cc_final: 0.4091 (tmt170) REVERT: B 692 ARG cc_start: 0.8627 (ttm110) cc_final: 0.8045 (ptp-170) REVERT: B 721 MET cc_start: 0.5242 (pmm) cc_final: 0.4974 (pmm) REVERT: D 407 MET cc_start: 0.7466 (mmm) cc_final: 0.7024 (mmm) REVERT: D 408 MET cc_start: 0.8648 (mmm) cc_final: 0.7664 (tpt) REVERT: D 424 TYR cc_start: 0.8409 (t80) cc_final: 0.8174 (t80) REVERT: D 519 ASP cc_start: 0.9258 (m-30) cc_final: 0.8853 (m-30) REVERT: D 590 ASP cc_start: 0.8695 (t70) cc_final: 0.8425 (t0) REVERT: E 10 MET cc_start: 0.8560 (mmm) cc_final: 0.8109 (tpt) REVERT: E 128 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: E 151 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9253 (tt) REVERT: E 160 ASN cc_start: 0.8723 (t0) cc_final: 0.8327 (t0) REVERT: E 203 ASP cc_start: 0.9156 (m-30) cc_final: 0.8682 (m-30) REVERT: F 61 SER cc_start: 0.9431 (t) cc_final: 0.9225 (p) REVERT: F 110 LEU cc_start: 0.8957 (tp) cc_final: 0.8608 (tp) REVERT: F 126 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8921 (mm-30) REVERT: F 185 LEU cc_start: 0.9387 (tp) cc_final: 0.9167 (tp) REVERT: F 192 MET cc_start: 0.8812 (mtt) cc_final: 0.8425 (mmp) REVERT: F 207 GLN cc_start: 0.9158 (tt0) cc_final: 0.8787 (tm-30) REVERT: G 41 LYS cc_start: 0.8333 (tmtt) cc_final: 0.8124 (tptt) REVERT: G 81 ASP cc_start: 0.8488 (t0) cc_final: 0.8277 (t0) REVERT: G 99 ARG cc_start: 0.8818 (mtt-85) cc_final: 0.8160 (mtm-85) REVERT: G 110 LEU cc_start: 0.9425 (tp) cc_final: 0.9087 (tp) REVERT: H 6 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7772 (ptm-80) REVERT: H 200 MET cc_start: 0.9203 (mtm) cc_final: 0.8680 (tpt) REVERT: H 207 GLN cc_start: 0.8796 (pp30) cc_final: 0.8590 (pp30) outliers start: 50 outliers final: 42 residues processed: 264 average time/residue: 0.1349 time to fit residues: 53.0031 Evaluate side-chains 268 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 627 GLU 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 613 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain B residue 811 LEU 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 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 128 TYR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR 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 155 VAL Chi-restraints excluded: chain F residue 195 VAL 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 G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 61 SER 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 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 45 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 124 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN B 619 ASN E 205 HIS F 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.132763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.081426 restraints weight = 81147.415| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.84 r_work: 0.2954 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 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 = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17434 Z= 0.140 Angle : 0.634 13.340 23684 Z= 0.318 Chirality : 0.040 0.264 2745 Planarity : 0.004 0.059 2906 Dihedral : 3.696 16.833 2434 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.23 % Allowed : 21.08 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.19), residues: 2229 helix: 2.75 (0.15), residues: 1349 sheet: -0.90 (0.44), residues: 151 loop : -0.90 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 453 TYR 0.020 0.001 TYR F 156 PHE 0.016 0.001 PHE A 682 TRP 0.062 0.001 TRP D 671 HIS 0.018 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00320 (17422) covalent geometry : angle 0.63385 (23660) SS BOND : bond 0.00296 ( 12) SS BOND : angle 0.99191 ( 24) hydrogen bonds : bond 0.03852 ( 1108) hydrogen bonds : angle 3.83183 ( 3282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5598.82 seconds wall clock time: 96 minutes 13.79 seconds (5773.79 seconds total)