Starting phenix.real_space_refine on Sun Jun 15 04:54:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3u_17395/06_2025/8p3u_17395_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3u_17395/06_2025/8p3u_17395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3u_17395/06_2025/8p3u_17395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3u_17395/06_2025/8p3u_17395.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3u_17395/06_2025/8p3u_17395_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3u_17395/06_2025/8p3u_17395_neut.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 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 96 5.16 5 C 11078 2.51 5 N 2735 2.21 5 O 2979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16888 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2850 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 2917 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 385, 2886 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Conformer: "B" Number of residues, atoms: 385, 2886 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 bond proxies already assigned to first conformer: 2915 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2848 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "D" Number of atoms: 2860 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 369} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 381, 2829 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 369} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 112 bond proxies already assigned to first conformer: 2855 Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1348 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1351 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE B 570 " occ=0.59 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.41 residue: pdb=" N AGLN B 582 " occ=0.24 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.76 residue: pdb=" N APHE B 619 " occ=0.37 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " occ=0.63 residue: pdb=" N APHE D 570 " occ=0.71 ... (20 atoms not shown) pdb=" CZ BPHE D 570 " occ=0.29 residue: pdb=" N AGLN D 582 " occ=0.10 ... (16 atoms not shown) pdb=" NE2BGLN D 582 " occ=0.90 residue: pdb=" N APHE D 619 " occ=0.68 ... (20 atoms not shown) pdb=" CZ BPHE D 619 " occ=0.32 Time building chain proxies: 13.52, per 1000 atoms: 0.80 Number of scatterers: 16888 At special positions: 0 Unit cell: (116.6, 117.925, 136.475, 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 96 16.00 O 2979 8.00 N 2735 7.00 C 11078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 3.2 seconds 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 26 sheets defined 61.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.593A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 4.163A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 542 removed outlier: 3.549A pdb=" N TRP A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 removed outlier: 3.878A pdb=" N MET A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 622 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.540A pdb=" N MET A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 804 " --> pdb=" O GLY A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.587A pdb=" N GLN B 410 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 419 through 433 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 518 through 542 removed outlier: 3.793A pdb=" N CYS B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 623 Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 649 through 657 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.556A pdb=" N SER B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 702 through 711 Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 784 through 787 removed outlier: 3.586A pdb=" N ASN B 787 " --> pdb=" O SER B 784 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 784 through 787' Processing helix chain 'B' and resid 788 through 815 removed outlier: 3.978A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.529A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.121A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.511A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 540 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 622 Processing helix chain 'C' and resid 632 through 638 removed outlier: 3.533A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.528A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.579A pdb=" N GLN D 410 " --> pdb=" O ASN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 removed outlier: 4.211A pdb=" N ASP D 415 " --> pdb=" O GLU D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 457 through 466 Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.515A pdb=" N LEU D 514 " --> pdb=" O PHE D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 542 removed outlier: 3.744A pdb=" N PHE D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 622 Processing helix chain 'D' and resid 631 through 638 Processing helix chain 'D' and resid 649 through 657 Processing helix chain 'D' and resid 660 through 673 Processing helix chain 'D' and resid 681 through 692 Processing helix chain 'D' and resid 702 through 711 Processing helix chain 'D' and resid 738 through 752 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 785 through 787 No H-bonds generated for 'chain 'D' and resid 785 through 787' Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.786A pdb=" N PHE D 792 " --> pdb=" O VAL D 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 93 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.315A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 4.242A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 3.688A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.590A pdb=" N VAL F 15 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 94 No H-bonds generated for 'chain 'F' and resid 93 through 94' Processing helix chain 'F' and resid 96 through 96 No H-bonds generated for 'chain 'F' and resid 96 through 96' Processing helix chain 'F' and resid 97 through 105 Processing helix chain 'F' and resid 105 through 124 removed outlier: 3.648A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.789A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.710A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 93 through 105 removed outlier: 3.548A pdb=" N ARG G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.508A pdb=" N CYS G 121 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 4.296A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.590A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 126 removed outlier: 4.045A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 4.042A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 removed outlier: 3.605A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.622A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 447 through 449 removed outlier: 3.671A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 494 removed outlier: 4.057A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.557A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 436 through 440 removed outlier: 6.758A pdb=" N TYR B 391 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU B 439 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL B 393 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 470 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.877A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.481A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.525A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 447 through 450 removed outlier: 3.753A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB7, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.847A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.541A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR C 698 " --> pdb=" O MET C 499 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 436 through 440 removed outlier: 6.397A pdb=" N TYR D 391 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLU D 439 " --> pdb=" O TYR D 391 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL D 393 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL D 470 " --> pdb=" O ILE D 392 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC2, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AC3, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.836A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 642 through 644 removed outlier: 6.620A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 removed outlier: 4.031A pdb=" N LYS E 78 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR E 66 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 34 through 38 Processing sheet with id=AC7, first strand: chain 'G' and resid 77 through 79 removed outlier: 4.126A pdb=" N LYS G 78 " --> pdb=" O THR G 66 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR G 66 " --> pdb=" O LYS G 78 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 77 through 79 1107 hydrogen bonds defined for protein. 3230 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: 6.59 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2617 1.32 - 1.44: 4983 1.44 - 1.57: 9525 1.57 - 1.70: 0 1.70 - 1.83: 156 Bond restraints: 17281 Sorted by residual: bond pdb=" C SER A 631 " pdb=" O SER A 631 " ideal model delta sigma weight residual 1.235 1.307 -0.072 1.26e-02 6.30e+03 3.26e+01 bond pdb=" C TYR D 391 " pdb=" O TYR D 391 " ideal model delta sigma weight residual 1.234 1.291 -0.057 1.34e-02 5.57e+03 1.82e+01 bond pdb=" N VAL C 484 " pdb=" CA VAL C 484 " ideal model delta sigma weight residual 1.456 1.497 -0.040 9.50e-03 1.11e+04 1.80e+01 bond pdb=" C ILE D 641 " pdb=" O ILE D 641 " ideal model delta sigma weight residual 1.234 1.282 -0.048 1.17e-02 7.31e+03 1.68e+01 bond pdb=" N VAL D 484 " pdb=" CA VAL D 484 " ideal model delta sigma weight residual 1.460 1.494 -0.034 8.60e-03 1.35e+04 1.59e+01 ... (remaining 17276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 23313 4.68 - 9.35: 134 9.35 - 14.03: 10 14.03 - 18.70: 5 18.70 - 23.38: 1 Bond angle restraints: 23463 Sorted by residual: angle pdb=" N LEU A 635 " pdb=" CA LEU A 635 " pdb=" C LEU A 635 " ideal model delta sigma weight residual 112.54 97.99 14.55 1.22e+00 6.72e-01 1.42e+02 angle pdb=" C LYS A 637 " pdb=" CA LYS A 637 " pdb=" CB LYS A 637 " ideal model delta sigma weight residual 110.42 87.04 23.38 1.99e+00 2.53e-01 1.38e+02 angle pdb=" C THR A 639 " pdb=" CA THR A 639 " pdb=" CB THR A 639 " ideal model delta sigma weight residual 110.36 95.23 15.13 1.78e+00 3.16e-01 7.23e+01 angle pdb=" C GLU C 630 " pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " ideal model delta sigma weight residual 110.42 93.95 16.47 1.99e+00 2.53e-01 6.85e+01 angle pdb=" N ILE A 641 " pdb=" CA ILE A 641 " pdb=" C ILE A 641 " ideal model delta sigma weight residual 109.34 93.67 15.67 2.08e+00 2.31e-01 5.67e+01 ... (remaining 23458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 8587 16.31 - 32.61: 992 32.61 - 48.92: 254 48.92 - 65.23: 64 65.23 - 81.53: 11 Dihedral angle restraints: 9908 sinusoidal: 3483 harmonic: 6425 Sorted by residual: dihedral pdb=" C LYS A 637 " pdb=" N LYS A 637 " pdb=" CA LYS A 637 " pdb=" CB LYS A 637 " ideal model delta harmonic sigma weight residual -122.60 -94.85 -27.75 0 2.50e+00 1.60e-01 1.23e+02 dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual 93.00 37.88 55.12 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" C GLU C 630 " pdb=" N GLU C 630 " pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " ideal model delta harmonic sigma weight residual -122.60 -106.57 -16.03 0 2.50e+00 1.60e-01 4.11e+01 ... (remaining 9905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1796 0.101 - 0.201: 842 0.201 - 0.302: 58 0.302 - 0.403: 13 0.403 - 0.503: 3 Chirality restraints: 2712 Sorted by residual: chirality pdb=" CA ILE B 500 " pdb=" N ILE B 500 " pdb=" C ILE B 500 " pdb=" CB ILE B 500 " both_signs ideal model delta sigma weight residual False 2.43 2.94 -0.50 2.00e-01 2.50e+01 6.33e+00 chirality pdb=" CA GLU A 630 " pdb=" N GLU A 630 " pdb=" C GLU A 630 " pdb=" CB GLU A 630 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CA LYS A 637 " pdb=" N LYS A 637 " pdb=" C LYS A 637 " pdb=" CB LYS A 637 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 2709 not shown) Planarity restraints: 2882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 630 " -0.037 2.00e-02 2.50e+03 7.69e-02 5.91e+01 pdb=" C GLU A 630 " 0.133 2.00e-02 2.50e+03 pdb=" O GLU A 630 " -0.050 2.00e-02 2.50e+03 pdb=" N SER A 631 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 632 " -0.025 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C ALA A 632 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA A 632 " -0.035 2.00e-02 2.50e+03 pdb=" N GLU A 633 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 633 " -0.024 2.00e-02 2.50e+03 5.08e-02 2.59e+01 pdb=" C GLU A 633 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU A 633 " -0.033 2.00e-02 2.50e+03 pdb=" N ASP A 634 " -0.030 2.00e-02 2.50e+03 ... (remaining 2879 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 715 2.71 - 3.26: 17907 3.26 - 3.81: 27007 3.81 - 4.35: 35054 4.35 - 4.90: 57095 Nonbonded interactions: 137778 Sorted by model distance: nonbonded pdb=" O ILE A 629 " pdb=" N SER A 631 " model vdw 2.166 3.120 nonbonded pdb=" O PHE D 580 " pdb=" OG1 THR D 605 " model vdw 2.170 3.040 nonbonded pdb=" O LYS B 501 " pdb=" O LYS B 502 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 631 " pdb=" N ALA A 632 " model vdw 2.228 3.120 nonbonded pdb=" O ALA A 636 " pdb=" N GLN A 638 " model vdw 2.232 3.120 ... (remaining 137773 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 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 414 or (resid 415 through 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 429 or (resid 4 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 431 through \ 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) or r \ esid 446 through 502 or resid 509 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 583 through 618 or resid 620 through 622 or resid 629 t \ hrough 664 or (resid 665 and (name N or name CA or name C or name O or name CB ) \ ) or resid 666 through 767 or resid 782 through 815)) selection = (chain 'B' and ((resid 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 403 or (resid 404 and (name \ N or name CA or name C or name O or name CB )) or resid 405 through 415 or (res \ id 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thr \ ough 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) \ or resid 431 through 444 or (resid 445 and (name N or name CA or name C or name \ O or name CB )) or resid 446 through 461 or (resid 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 500 or (resid 501 through 5 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 509 through \ 545 or (resid 566 and (name N or name CA or name C or name O or name CB )) or r \ esid 567 through 569 or resid 571 through 581 or resid 583 through 618 or resid \ 620 through 622 or resid 629 through 632 or (resid 633 through 634 and (name N o \ r name CA or name C or name O or name CB )) or resid 635 through 658 or (resid 6 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 660 through \ 664 or (resid 665 and (name N or name CA or name C or name O or name CB )) or r \ esid 666 through 683 or (resid 684 and (name N or name CA or name C or name O or \ name CB )) or resid 685 through 687 or (resid 688 and (name N or name CA or nam \ e C or name O or name CB )) or resid 689 through 690 or (resid 691 through 693 a \ nd (name N or name CA or name C or name O or name CB )) or resid 694 through 705 \ or (resid 706 and (name N or name CA or name C or name O or name CB )) or resid \ 707 through 767 or resid 782 through 813 or (resid 814 through 815 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 390 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 415 or (resid 416 and (name \ N or name CA or name C or name O or name CB )) or resid 417 through 466 or (res \ id 467 through 469 and (name N or name CA or name C or name O or name CB )) or r \ esid 470 through 502 or resid 509 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 583 through 618 or resid 620 through 622 or resid 629 t \ hrough 633 or (resid 634 and (name N or name CA or name C or name O or name CB ) \ ) or resid 635 through 687 or (resid 688 and (name N or name CA or name C or nam \ e O or name CB )) or resid 689 through 691 or (resid 692 through 693 and (name N \ or name CA or name C or name O or name CB )) or resid 694 through 708 or (resid \ 709 and (name N or name CA or name C or name O or name CB )) or resid 710 throu \ gh 815)) selection = (chain 'D' and (resid 390 through 444 or (resid 445 and (name N or name CA or na \ me C or name O or name CB )) or resid 446 through 466 or (resid 467 through 469 \ and (name N or name CA or name C or name O or name CB )) or resid 470 through 54 \ 5 or (resid 566 and (name N or name CA or name C or name O or name CB )) or resi \ d 567 through 569 or resid 571 through 581 or resid 583 through 618 or resid 620 \ through 658 or (resid 659 and (name N or name CA or name C or name O or name CB \ )) or resid 660 through 664 or (resid 665 and (name N or name CA or name C or n \ ame O or name CB )) or resid 666 through 687 or (resid 688 and (name N or name C \ A or name C or name O or name CB )) or resid 689 through 691 or (resid 692 throu \ gh 693 and (name N or name CA or name C or name O or name CB )) or resid 694 thr \ ough 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) \ or resid 707 through 708 or (resid 709 and (name N or name CA or name C or name \ O or name CB )) or resid 710 through 767 or resid 782 through 813 or (resid 814 \ through 815 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'E' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 94 or resid 96 through 209)) selection = (chain 'F' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 209)) selection = (chain 'G' and (resid 5 through 94 or resid 96 through 209)) selection = (chain 'H' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 94 or resid 96 through 209)) } 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=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.260 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 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 : 0.012 0.072 17289 Z= 0.857 Angle : 1.426 23.378 23479 Z= 1.035 Chirality : 0.102 0.503 2712 Planarity : 0.011 0.200 2882 Dihedral : 15.167 81.533 5782 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.54 % Favored : 96.86 % Rotamer: Outliers : 3.81 % Allowed : 16.62 % Favored : 79.57 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2185 helix: 0.91 (0.13), residues: 1307 sheet: -2.31 (0.36), residues: 156 loop : -0.98 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 601 HIS 0.006 0.002 HIS F 60 PHE 0.033 0.002 PHE B 663 TYR 0.022 0.003 TYR A 417 ARG 0.013 0.001 ARG C 416 Details of bonding type rmsd hydrogen bonds : bond 0.20414 ( 1107) hydrogen bonds : angle 6.04437 ( 3230) SS BOND : bond 0.00285 ( 8) SS BOND : angle 1.00931 ( 16) covalent geometry : bond 0.01154 (17281) covalent geometry : angle 1.42633 (23463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 247 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 795 LEU cc_start: 0.9355 (tp) cc_final: 0.9054 (tt) REVERT: C 484 VAL cc_start: -0.0665 (OUTLIER) cc_final: -0.1483 (p) REVERT: C 605 THR cc_start: 0.9020 (m) cc_final: 0.8555 (m) REVERT: C 611 SER cc_start: 0.9606 (m) cc_final: 0.9352 (p) REVERT: D 615 ASN cc_start: 0.8616 (t0) cc_final: 0.8175 (t0) REVERT: E 10 MET cc_start: 0.8443 (tpt) cc_final: 0.8023 (tpt) REVERT: E 81 ASP cc_start: 0.7525 (t0) cc_final: 0.7232 (t0) REVERT: E 97 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9233 (tt) REVERT: F 58 MET cc_start: 0.8325 (mmm) cc_final: 0.7834 (tpp) REVERT: G 136 LEU cc_start: 0.8866 (tp) cc_final: 0.8635 (pp) REVERT: H 81 ASP cc_start: 0.8173 (t0) cc_final: 0.7813 (t0) outliers start: 62 outliers final: 26 residues processed: 292 average time/residue: 0.2966 time to fit residues: 133.4399 Evaluate side-chains 195 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 499 MET Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A 638 GLN C 431 HIS ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.102776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.074085 restraints weight = 248366.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.076842 restraints weight = 101947.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.078743 restraints weight = 59244.589| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17289 Z= 0.143 Angle : 0.611 8.898 23479 Z= 0.317 Chirality : 0.041 0.240 2712 Planarity : 0.004 0.036 2882 Dihedral : 5.235 55.896 2461 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.43 % Favored : 98.34 % Rotamer: Outliers : 3.22 % Allowed : 18.88 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.18), residues: 2185 helix: 2.19 (0.14), residues: 1329 sheet: -1.93 (0.35), residues: 168 loop : -0.63 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 601 HIS 0.006 0.001 HIS F 60 PHE 0.019 0.001 PHE D 542 TYR 0.020 0.001 TYR C 420 ARG 0.006 0.000 ARG C 739 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 1107) hydrogen bonds : angle 4.10464 ( 3230) SS BOND : bond 0.00213 ( 8) SS BOND : angle 1.44676 ( 16) covalent geometry : bond 0.00303 (17281) covalent geometry : angle 0.60980 (23463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 1.810 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 459 MET cc_start: 0.5547 (mpp) cc_final: 0.5292 (mpp) REVERT: A 538 LEU cc_start: 0.9430 (tp) cc_final: 0.9172 (tt) REVERT: A 581 MET cc_start: 0.8115 (mpp) cc_final: 0.7679 (mpp) REVERT: A 601 TRP cc_start: 0.8301 (t-100) cc_final: 0.8095 (t-100) REVERT: A 795 LEU cc_start: 0.9415 (tp) cc_final: 0.9213 (tt) REVERT: C 484 VAL cc_start: 0.0650 (OUTLIER) cc_final: -0.0075 (m) REVERT: C 605 THR cc_start: 0.8959 (m) cc_final: 0.8563 (m) REVERT: C 704 MET cc_start: 0.8610 (mpp) cc_final: 0.8149 (mpp) REVERT: D 615 ASN cc_start: 0.8678 (t0) cc_final: 0.8317 (t0) REVERT: D 714 CYS cc_start: 0.9032 (t) cc_final: 0.8536 (m) REVERT: E 81 ASP cc_start: 0.7650 (t0) cc_final: 0.7335 (t0) REVERT: F 24 MET cc_start: 0.8781 (tpt) cc_final: 0.8061 (tpt) REVERT: F 58 MET cc_start: 0.8307 (mmm) cc_final: 0.8046 (tpp) REVERT: F 81 ASP cc_start: 0.8562 (t0) cc_final: 0.8344 (t0) REVERT: G 70 GLU cc_start: 0.7342 (mp0) cc_final: 0.7109 (mp0) REVERT: G 206 GLN cc_start: 0.9250 (pt0) cc_final: 0.8981 (pp30) REVERT: H 81 ASP cc_start: 0.8040 (t0) cc_final: 0.7620 (t0) REVERT: H 207 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8465 (mt) outliers start: 52 outliers final: 23 residues processed: 233 average time/residue: 0.2609 time to fit residues: 97.9932 Evaluate side-chains 190 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 110 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 139 optimal weight: 50.0000 chunk 192 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 752 GLN B 743 ASN C 582 GLN C 583 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.094376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.066461 restraints weight = 231284.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.068775 restraints weight = 104518.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.070260 restraints weight = 62929.211| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17289 Z= 0.284 Angle : 0.736 9.413 23479 Z= 0.389 Chirality : 0.044 0.215 2712 Planarity : 0.004 0.048 2882 Dihedral : 4.962 51.791 2424 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.08 % Favored : 97.69 % Rotamer: Outliers : 4.76 % Allowed : 19.18 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.18), residues: 2185 helix: 1.86 (0.14), residues: 1331 sheet: -1.79 (0.35), residues: 191 loop : -0.44 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 601 HIS 0.020 0.002 HIS A 431 PHE 0.024 0.002 PHE B 580 TYR 0.023 0.002 TYR C 728 ARG 0.009 0.001 ARG C 688 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 1107) hydrogen bonds : angle 4.60707 ( 3230) SS BOND : bond 0.00375 ( 8) SS BOND : angle 1.54517 ( 16) covalent geometry : bond 0.00614 (17281) covalent geometry : angle 0.73541 (23463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 154 time to evaluate : 2.188 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 403 MET cc_start: 0.6396 (mpp) cc_final: 0.5992 (mpp) REVERT: A 492 MET cc_start: 0.7376 (tpp) cc_final: 0.7150 (tpp) REVERT: A 511 PHE cc_start: 0.5509 (OUTLIER) cc_final: 0.3794 (p90) REVERT: A 581 MET cc_start: 0.8359 (mpp) cc_final: 0.7754 (mpp) REVERT: B 581 MET cc_start: 0.9093 (mmp) cc_final: 0.8639 (mmm) REVERT: C 403 MET cc_start: 0.4025 (mpp) cc_final: 0.3785 (mpp) REVERT: C 704 MET cc_start: 0.8638 (mpp) cc_final: 0.8117 (mpp) REVERT: D 615 ASN cc_start: 0.8729 (t0) cc_final: 0.8394 (t0) REVERT: E 81 ASP cc_start: 0.7567 (t0) cc_final: 0.7219 (t0) REVERT: E 188 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8760 (pt) REVERT: F 204 HIS cc_start: 0.6072 (OUTLIER) cc_final: 0.5708 (m170) REVERT: G 81 ASP cc_start: 0.8589 (t0) cc_final: 0.8289 (t0) REVERT: G 190 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8325 (mm-30) REVERT: G 204 HIS cc_start: 0.6086 (OUTLIER) cc_final: 0.5108 (m-70) REVERT: H 81 ASP cc_start: 0.8016 (t0) cc_final: 0.7641 (t0) outliers start: 80 outliers final: 46 residues processed: 221 average time/residue: 0.2912 time to fit residues: 104.7429 Evaluate side-chains 197 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 4.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 157 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 135 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 179 optimal weight: 0.0970 chunk 34 optimal weight: 6.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 GLN C 583 GLN D 743 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.096752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.068472 restraints weight = 260161.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071063 restraints weight = 106221.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.072787 restraints weight = 61891.644| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17289 Z= 0.172 Angle : 0.620 9.792 23479 Z= 0.319 Chirality : 0.041 0.180 2712 Planarity : 0.004 0.050 2882 Dihedral : 4.417 50.927 2420 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.62 % Favored : 98.15 % Rotamer: Outliers : 4.23 % Allowed : 21.32 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 2185 helix: 2.12 (0.14), residues: 1329 sheet: -1.58 (0.35), residues: 196 loop : -0.38 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 763 HIS 0.005 0.001 HIS A 431 PHE 0.015 0.001 PHE B 580 TYR 0.017 0.001 TYR C 728 ARG 0.006 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 1107) hydrogen bonds : angle 4.23017 ( 3230) SS BOND : bond 0.00453 ( 8) SS BOND : angle 1.92268 ( 16) covalent geometry : bond 0.00383 (17281) covalent geometry : angle 0.61834 (23463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 158 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.8459 (mpp) cc_final: 0.7942 (mpp) REVERT: A 582 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: B 686 MET cc_start: 0.8690 (tpp) cc_final: 0.8469 (tpp) REVERT: B 704 MET cc_start: 0.8327 (tpt) cc_final: 0.7951 (mmm) REVERT: C 403 MET cc_start: 0.3704 (mpp) cc_final: 0.3204 (mpp) REVERT: C 605 THR cc_start: 0.8961 (m) cc_final: 0.8600 (m) REVERT: C 704 MET cc_start: 0.8655 (mpp) cc_final: 0.8262 (mpp) REVERT: D 443 ASP cc_start: 0.6737 (m-30) cc_final: 0.6504 (t0) REVERT: D 615 ASN cc_start: 0.8778 (t0) cc_final: 0.8445 (t0) REVERT: D 743 ASN cc_start: 0.3632 (OUTLIER) cc_final: 0.3360 (m-40) REVERT: E 81 ASP cc_start: 0.7759 (t0) cc_final: 0.7434 (t0) REVERT: F 58 MET cc_start: 0.8561 (tpp) cc_final: 0.7993 (tpp) REVERT: G 190 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8371 (mm-30) REVERT: G 204 HIS cc_start: 0.6163 (OUTLIER) cc_final: 0.4896 (m-70) REVERT: G 206 GLN cc_start: 0.9209 (pt0) cc_final: 0.8966 (pp30) REVERT: H 10 MET cc_start: 0.8732 (ppp) cc_final: 0.8382 (ppp) REVERT: H 81 ASP cc_start: 0.7955 (t0) cc_final: 0.7693 (t0) REVERT: H 113 THR cc_start: 0.9404 (m) cc_final: 0.9166 (p) REVERT: H 204 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7591 (m-70) outliers start: 69 outliers final: 41 residues processed: 209 average time/residue: 0.2529 time to fit residues: 84.6751 Evaluate side-chains 193 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 583 GLN Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 743 ASN Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 583 GLN D 743 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.097239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.069186 restraints weight = 253124.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.071745 restraints weight = 104813.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.073631 restraints weight = 60927.923| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17289 Z= 0.142 Angle : 0.603 11.454 23479 Z= 0.307 Chirality : 0.040 0.177 2712 Planarity : 0.004 0.051 2882 Dihedral : 4.155 50.797 2418 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.98 % Favored : 97.83 % Rotamer: Outliers : 4.11 % Allowed : 21.74 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.18), residues: 2185 helix: 2.23 (0.14), residues: 1332 sheet: -1.44 (0.35), residues: 198 loop : -0.36 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 601 HIS 0.007 0.001 HIS G 204 PHE 0.014 0.001 PHE C 580 TYR 0.021 0.001 TYR B 728 ARG 0.006 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 1107) hydrogen bonds : angle 4.11540 ( 3230) SS BOND : bond 0.00448 ( 8) SS BOND : angle 1.61415 ( 16) covalent geometry : bond 0.00315 (17281) covalent geometry : angle 0.60208 (23463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 160 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 PHE cc_start: 0.5520 (OUTLIER) cc_final: 0.3820 (p90) REVERT: A 538 LEU cc_start: 0.9387 (tp) cc_final: 0.9153 (tt) REVERT: A 581 MET cc_start: 0.8340 (mpp) cc_final: 0.8006 (mpp) REVERT: A 582 GLN cc_start: 0.6890 (tm-30) cc_final: 0.6630 (tm-30) REVERT: B 704 MET cc_start: 0.8207 (tpt) cc_final: 0.7960 (mmm) REVERT: C 403 MET cc_start: 0.3763 (mpp) cc_final: 0.3265 (mpp) REVERT: C 605 THR cc_start: 0.8905 (m) cc_final: 0.8582 (m) REVERT: C 704 MET cc_start: 0.8628 (mpp) cc_final: 0.8189 (mpp) REVERT: D 615 ASN cc_start: 0.8831 (t0) cc_final: 0.8491 (t0) REVERT: D 743 ASN cc_start: 0.3066 (OUTLIER) cc_final: 0.2704 (m-40) REVERT: E 81 ASP cc_start: 0.7833 (t0) cc_final: 0.7539 (t0) REVERT: E 153 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9274 (mp) REVERT: F 58 MET cc_start: 0.8615 (tpp) cc_final: 0.8140 (tpp) REVERT: G 190 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8397 (mm-30) REVERT: G 206 GLN cc_start: 0.9137 (pt0) cc_final: 0.8935 (pp30) REVERT: H 10 MET cc_start: 0.8774 (ppp) cc_final: 0.8526 (ppp) REVERT: H 34 LEU cc_start: 0.8708 (tp) cc_final: 0.8389 (tp) REVERT: H 81 ASP cc_start: 0.7924 (t0) cc_final: 0.7651 (t0) REVERT: H 113 THR cc_start: 0.9417 (m) cc_final: 0.9199 (p) REVERT: H 181 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: H 204 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7513 (m-70) outliers start: 67 outliers final: 44 residues processed: 211 average time/residue: 0.2976 time to fit residues: 101.9259 Evaluate side-chains 201 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 743 ASN Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 39 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 196 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 583 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.094134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.066684 restraints weight = 223065.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.068814 restraints weight = 101021.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.070380 restraints weight = 60083.066| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17289 Z= 0.205 Angle : 0.652 14.902 23479 Z= 0.333 Chirality : 0.041 0.184 2712 Planarity : 0.004 0.053 2882 Dihedral : 4.300 48.928 2418 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.35 % Favored : 97.51 % Rotamer: Outliers : 4.76 % Allowed : 21.02 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2185 helix: 2.04 (0.14), residues: 1336 sheet: -1.73 (0.42), residues: 132 loop : -0.45 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 601 HIS 0.005 0.001 HIS G 204 PHE 0.020 0.001 PHE B 580 TYR 0.020 0.002 TYR B 728 ARG 0.010 0.001 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 1107) hydrogen bonds : angle 4.34256 ( 3230) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.43788 ( 16) covalent geometry : bond 0.00450 (17281) covalent geometry : angle 0.65101 (23463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 148 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.6523 (mpp) cc_final: 0.6231 (mpp) REVERT: A 459 MET cc_start: 0.6518 (mmt) cc_final: 0.6165 (mmp) REVERT: A 511 PHE cc_start: 0.5076 (OUTLIER) cc_final: 0.4042 (p90) REVERT: A 581 MET cc_start: 0.8446 (mpp) cc_final: 0.8190 (mpp) REVERT: C 403 MET cc_start: 0.4088 (mpp) cc_final: 0.3798 (mpp) REVERT: C 583 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8382 (tp40) REVERT: C 605 THR cc_start: 0.8954 (m) cc_final: 0.8637 (m) REVERT: C 686 MET cc_start: 0.8770 (ppp) cc_final: 0.8417 (ppp) REVERT: C 704 MET cc_start: 0.8697 (mpp) cc_final: 0.8213 (mpp) REVERT: D 615 ASN cc_start: 0.8728 (t0) cc_final: 0.8361 (t0) REVERT: E 81 ASP cc_start: 0.7731 (t0) cc_final: 0.7442 (t0) REVERT: E 153 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9273 (mp) REVERT: F 58 MET cc_start: 0.8547 (tpp) cc_final: 0.8115 (tpp) REVERT: G 190 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8291 (mm-30) REVERT: G 204 HIS cc_start: 0.5440 (OUTLIER) cc_final: 0.4828 (m-70) REVERT: H 10 MET cc_start: 0.8781 (ppp) cc_final: 0.8572 (ppp) REVERT: H 81 ASP cc_start: 0.8175 (t0) cc_final: 0.7959 (t0) REVERT: H 113 THR cc_start: 0.9423 (m) cc_final: 0.9183 (p) REVERT: H 181 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: H 204 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7614 (m-70) outliers start: 78 outliers final: 48 residues processed: 213 average time/residue: 0.3152 time to fit residues: 110.7065 Evaluate side-chains 195 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 583 GLN Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 214 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 50.0000 chunk 145 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 204 HIS ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.089513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.061795 restraints weight = 234590.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.064106 restraints weight = 102428.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.065458 restraints weight = 60996.510| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 17289 Z= 0.334 Angle : 0.805 12.473 23479 Z= 0.418 Chirality : 0.046 0.191 2712 Planarity : 0.005 0.049 2882 Dihedral : 5.026 45.794 2418 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 5.36 % Allowed : 21.38 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2185 helix: 1.40 (0.14), residues: 1309 sheet: -1.88 (0.49), residues: 99 loop : -0.82 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 601 HIS 0.007 0.001 HIS G 204 PHE 0.028 0.002 PHE B 678 TYR 0.025 0.002 TYR A 519 ARG 0.017 0.001 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 1107) hydrogen bonds : angle 5.03508 ( 3230) SS BOND : bond 0.00324 ( 8) SS BOND : angle 1.68088 ( 16) covalent geometry : bond 0.00724 (17281) covalent geometry : angle 0.80436 (23463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 134 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 PHE cc_start: 0.4742 (OUTLIER) cc_final: 0.3527 (p90) REVERT: A 581 MET cc_start: 0.8485 (mpp) cc_final: 0.7990 (mpp) REVERT: B 686 MET cc_start: 0.8849 (tpp) cc_final: 0.8608 (tpp) REVERT: C 686 MET cc_start: 0.9030 (ppp) cc_final: 0.8684 (ppp) REVERT: D 615 ASN cc_start: 0.8703 (t0) cc_final: 0.8378 (t0) REVERT: E 81 ASP cc_start: 0.7326 (t0) cc_final: 0.7041 (t0) REVERT: F 24 MET cc_start: 0.9285 (tpt) cc_final: 0.8342 (tpt) REVERT: F 82 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7030 (m170) REVERT: G 81 ASP cc_start: 0.8536 (t0) cc_final: 0.8309 (t0) REVERT: G 190 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8453 (mm-30) REVERT: G 204 HIS cc_start: 0.5855 (OUTLIER) cc_final: 0.4808 (m90) REVERT: H 117 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7965 (t80) REVERT: H 181 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: H 204 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6901 (m-70) outliers start: 88 outliers final: 66 residues processed: 205 average time/residue: 0.2458 time to fit residues: 82.0190 Evaluate side-chains 203 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 131 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 519 TYR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 801 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 18 PHE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 117 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 77 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 199 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 HIS ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.092024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063964 restraints weight = 278612.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.066322 restraints weight = 112866.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.068011 restraints weight = 64419.024| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17289 Z= 0.213 Angle : 0.692 11.526 23479 Z= 0.353 Chirality : 0.043 0.231 2712 Planarity : 0.004 0.050 2882 Dihedral : 4.575 45.731 2416 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.68 % Favored : 97.19 % Rotamer: Outliers : 4.29 % Allowed : 23.05 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2185 helix: 1.63 (0.14), residues: 1323 sheet: -1.96 (0.48), residues: 109 loop : -0.78 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 601 HIS 0.007 0.001 HIS G 204 PHE 0.017 0.001 PHE C 491 TYR 0.018 0.002 TYR A 519 ARG 0.011 0.001 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1107) hydrogen bonds : angle 4.63252 ( 3230) SS BOND : bond 0.00290 ( 8) SS BOND : angle 1.69078 ( 16) covalent geometry : bond 0.00474 (17281) covalent geometry : angle 0.69110 (23463) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 139 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.6646 (mpp) cc_final: 0.6407 (mpp) REVERT: A 511 PHE cc_start: 0.4755 (OUTLIER) cc_final: 0.3626 (p90) REVERT: A 581 MET cc_start: 0.8595 (mpp) cc_final: 0.8195 (mpp) REVERT: A 582 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: A 637 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7273 (pttt) REVERT: B 659 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7601 (mptt) REVERT: B 686 MET cc_start: 0.8875 (tpp) cc_final: 0.8668 (tpp) REVERT: C 403 MET cc_start: 0.4430 (OUTLIER) cc_final: 0.4221 (mpp) REVERT: C 605 THR cc_start: 0.8983 (m) cc_final: 0.8650 (m) REVERT: C 686 MET cc_start: 0.8979 (ppp) cc_final: 0.8642 (ppp) REVERT: C 704 MET cc_start: 0.8336 (mpp) cc_final: 0.7692 (mpp) REVERT: C 717 MET cc_start: 0.7811 (ptt) cc_final: 0.6688 (mmp) REVERT: D 499 MET cc_start: 0.3299 (tmm) cc_final: 0.2915 (ppp) REVERT: D 615 ASN cc_start: 0.8782 (t0) cc_final: 0.8417 (t0) REVERT: E 81 ASP cc_start: 0.7457 (t0) cc_final: 0.7210 (t0) REVERT: F 24 MET cc_start: 0.9112 (tpt) cc_final: 0.8060 (tpt) REVERT: F 58 MET cc_start: 0.8779 (tpp) cc_final: 0.8161 (tpp) REVERT: G 190 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8432 (mm-30) REVERT: G 204 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.5201 (m90) REVERT: H 181 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: H 204 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6941 (m-70) outliers start: 70 outliers final: 53 residues processed: 195 average time/residue: 0.2301 time to fit residues: 74.3118 Evaluate side-chains 199 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 138 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 519 TYR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 118 optimal weight: 40.0000 chunk 75 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 135 optimal weight: 0.0470 chunk 153 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.093893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.066456 restraints weight = 216603.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.068770 restraints weight = 97971.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.070285 restraints weight = 57718.405| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17289 Z= 0.151 Angle : 0.659 11.595 23479 Z= 0.329 Chirality : 0.042 0.215 2712 Planarity : 0.004 0.049 2882 Dihedral : 4.310 44.033 2416 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.54 % Favored : 97.32 % Rotamer: Outliers : 3.39 % Allowed : 23.76 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2185 helix: 1.96 (0.14), residues: 1322 sheet: -1.93 (0.52), residues: 96 loop : -0.79 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 601 HIS 0.004 0.001 HIS G 60 PHE 0.029 0.001 PHE B 678 TYR 0.017 0.001 TYR H 175 ARG 0.010 0.001 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 1107) hydrogen bonds : angle 4.36723 ( 3230) SS BOND : bond 0.00557 ( 8) SS BOND : angle 2.01061 ( 16) covalent geometry : bond 0.00340 (17281) covalent geometry : angle 0.65761 (23463) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.5601 (mmp) cc_final: 0.4903 (mmp) REVERT: A 511 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.3600 (p90) REVERT: A 538 LEU cc_start: 0.9376 (tp) cc_final: 0.9171 (tt) REVERT: A 581 MET cc_start: 0.8597 (mpp) cc_final: 0.8332 (mpp) REVERT: A 582 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6480 (tm-30) REVERT: B 686 MET cc_start: 0.8867 (tpp) cc_final: 0.8660 (tpp) REVERT: C 403 MET cc_start: 0.4472 (OUTLIER) cc_final: 0.4219 (mpp) REVERT: C 605 THR cc_start: 0.8931 (m) cc_final: 0.8578 (m) REVERT: C 686 MET cc_start: 0.8909 (ppp) cc_final: 0.8665 (ppp) REVERT: C 704 MET cc_start: 0.8221 (mpp) cc_final: 0.7487 (mpp) REVERT: C 717 MET cc_start: 0.7661 (ptt) cc_final: 0.6619 (mmt) REVERT: D 499 MET cc_start: 0.3418 (tmm) cc_final: 0.3104 (ppp) REVERT: D 615 ASN cc_start: 0.8804 (t0) cc_final: 0.8449 (t0) REVERT: E 81 ASP cc_start: 0.7499 (t0) cc_final: 0.7285 (t0) REVERT: E 190 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8658 (tm-30) REVERT: F 58 MET cc_start: 0.8709 (tpp) cc_final: 0.8115 (tpp) REVERT: G 190 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8299 (mm-30) REVERT: H 113 THR cc_start: 0.9455 (m) cc_final: 0.9224 (p) REVERT: H 117 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7917 (t80) REVERT: H 147 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9404 (mt) REVERT: H 181 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: H 204 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7801 (m-70) outliers start: 55 outliers final: 43 residues processed: 188 average time/residue: 0.2343 time to fit residues: 73.6215 Evaluate side-chains 190 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 117 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 196 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 90 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.093944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.066376 restraints weight = 285091.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.068634 restraints weight = 115342.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.070426 restraints weight = 64333.541| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17289 Z= 0.155 Angle : 0.677 12.550 23479 Z= 0.337 Chirality : 0.042 0.214 2712 Planarity : 0.004 0.050 2882 Dihedral : 4.295 45.614 2416 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.58 % Favored : 97.28 % Rotamer: Outliers : 3.51 % Allowed : 24.24 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.18), residues: 2185 helix: 1.98 (0.14), residues: 1325 sheet: -2.20 (0.48), residues: 111 loop : -0.68 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 601 HIS 0.004 0.001 HIS G 60 PHE 0.023 0.001 PHE B 678 TYR 0.019 0.001 TYR H 175 ARG 0.009 0.001 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1107) hydrogen bonds : angle 4.34698 ( 3230) SS BOND : bond 0.00518 ( 8) SS BOND : angle 1.94228 ( 16) covalent geometry : bond 0.00350 (17281) covalent geometry : angle 0.67506 (23463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 145 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.5436 (mmp) cc_final: 0.4647 (mmp) REVERT: A 511 PHE cc_start: 0.4701 (OUTLIER) cc_final: 0.3624 (p90) REVERT: A 581 MET cc_start: 0.8683 (mpp) cc_final: 0.8476 (mpp) REVERT: A 582 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: B 492 MET cc_start: 0.6122 (ppp) cc_final: 0.5852 (ppp) REVERT: B 515 ASP cc_start: 0.8537 (p0) cc_final: 0.8079 (p0) REVERT: B 686 MET cc_start: 0.8810 (tpp) cc_final: 0.8543 (tpp) REVERT: C 403 MET cc_start: 0.4321 (OUTLIER) cc_final: 0.4062 (mpp) REVERT: C 499 MET cc_start: 0.6508 (mmm) cc_final: 0.6143 (mmt) REVERT: C 686 MET cc_start: 0.8877 (ppp) cc_final: 0.8639 (ppp) REVERT: C 704 MET cc_start: 0.8369 (mpp) cc_final: 0.7727 (mpp) REVERT: C 717 MET cc_start: 0.7854 (ptt) cc_final: 0.6874 (mmt) REVERT: D 499 MET cc_start: 0.3042 (tmm) cc_final: 0.2749 (ppp) REVERT: D 615 ASN cc_start: 0.8771 (t0) cc_final: 0.8407 (t0) REVERT: E 81 ASP cc_start: 0.7550 (t0) cc_final: 0.7301 (t0) REVERT: E 148 SER cc_start: 0.9374 (OUTLIER) cc_final: 0.9173 (p) REVERT: F 58 MET cc_start: 0.8599 (tpp) cc_final: 0.8044 (tpp) REVERT: G 190 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8282 (mm-30) REVERT: H 113 THR cc_start: 0.9472 (m) cc_final: 0.9234 (p) REVERT: H 117 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7932 (t80) REVERT: H 147 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9407 (mt) REVERT: H 181 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: H 204 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7750 (m-70) outliers start: 57 outliers final: 46 residues processed: 185 average time/residue: 0.2850 time to fit residues: 89.0292 Evaluate side-chains 199 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 117 PHE Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 127 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 43 optimal weight: 0.0060 chunk 124 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 140 optimal weight: 0.0050 chunk 53 optimal weight: 8.9990 overall best weight: 4.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.091525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.064214 restraints weight = 239942.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.066452 restraints weight = 101160.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.068085 restraints weight = 59945.876| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17289 Z= 0.225 Angle : 0.729 12.116 23479 Z= 0.367 Chirality : 0.043 0.229 2712 Planarity : 0.004 0.049 2882 Dihedral : 4.520 51.007 2416 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 3.57 % Allowed : 24.30 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2185 helix: 1.77 (0.14), residues: 1324 sheet: -2.12 (0.51), residues: 103 loop : -0.71 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 601 HIS 0.005 0.001 HIS G 204 PHE 0.020 0.002 PHE B 678 TYR 0.020 0.002 TYR H 175 ARG 0.009 0.001 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 1107) hydrogen bonds : angle 4.59685 ( 3230) SS BOND : bond 0.00493 ( 8) SS BOND : angle 1.94427 ( 16) covalent geometry : bond 0.00500 (17281) covalent geometry : angle 0.72759 (23463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7002.22 seconds wall clock time: 125 minutes 11.82 seconds (7511.82 seconds total)