Starting phenix.real_space_refine on Sun Aug 24 04:23:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3u_17395/08_2025/8p3u_17395_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3u_17395/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p3u_17395/08_2025/8p3u_17395_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3u_17395/08_2025/8p3u_17395_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p3u_17395/08_2025/8p3u_17395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3u_17395/08_2025/8p3u_17395.map" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 13, 'ARG:plan': 6, 'TYR:plan': 2, 'TRP:plan': 1} 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: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 2} 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: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 2} 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: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 13, 'ASP:plan': 5, 'ARG:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1} 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: {'TYR:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 1, '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: {'TYR:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 1, '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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE: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: {'ARG:plan': 1, 'GLU: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: 4.88, per 1000 atoms: 0.29 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: 1.45 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.39 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: 3.94 Time building geometry restraints manager: 1.95 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.580 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- 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 : 13.36 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (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 ARG 0.013 0.001 ARG C 416 TYR 0.022 0.003 TYR A 417 PHE 0.033 0.002 PHE B 663 TRP 0.024 0.003 TRP A 601 HIS 0.006 0.002 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.01154 (17281) covalent geometry : angle 1.42633 (23463) SS BOND : bond 0.00285 ( 8) SS BOND : angle 1.00931 ( 16) hydrogen bonds : bond 0.20414 ( 1107) hydrogen bonds : angle 6.04437 ( 3230) *********************** 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 : 0.756 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: 0.1096 time to fit residues: 49.7531 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 : 0.636 ------------------------------------------------------------------------------- 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 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0060 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- 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 B 743 ASN C 431 HIS 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** ** G 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 = 0.4241 r_free = 0.4241 target = 0.102753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.074430 restraints weight = 221832.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.077025 restraints weight = 95804.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.078835 restraints weight = 57141.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080124 restraints weight = 40080.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.080974 restraints weight = 31103.496| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2305 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= 0.140 Angle : 0.609 8.981 23479 Z= 0.316 Chirality : 0.041 0.242 2712 Planarity : 0.004 0.037 2882 Dihedral : 5.238 56.206 2461 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.38 % Favored : 98.38 % Rotamer: Outliers : 3.28 % Allowed : 19.06 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.18), residues: 2185 helix: 2.15 (0.14), residues: 1335 sheet: -1.89 (0.35), residues: 167 loop : -0.60 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 739 TYR 0.021 0.001 TYR C 420 PHE 0.019 0.001 PHE D 542 TRP 0.030 0.001 TRP A 601 HIS 0.006 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00298 (17281) covalent geometry : angle 0.60813 (23463) SS BOND : bond 0.00736 ( 8) SS BOND : angle 1.66742 ( 16) hydrogen bonds : bond 0.04456 ( 1107) hydrogen bonds : angle 4.11302 ( 3230) *********************** 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: 53 poor density : 195 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.5860 (mpp) cc_final: 0.5526 (mpp) REVERT: A 538 LEU cc_start: 0.9438 (tp) cc_final: 0.9187 (tt) REVERT: A 581 MET cc_start: 0.8203 (mpp) cc_final: 0.7770 (mpp) REVERT: A 601 TRP cc_start: 0.8337 (t-100) cc_final: 0.8128 (t-100) REVERT: A 794 ILE cc_start: 0.9396 (mt) cc_final: 0.9196 (mm) REVERT: C 499 MET cc_start: 0.6301 (ttt) cc_final: 0.5844 (tpp) REVERT: C 605 THR cc_start: 0.8935 (m) cc_final: 0.8526 (m) REVERT: C 611 SER cc_start: 0.9577 (m) cc_final: 0.9341 (p) REVERT: C 704 MET cc_start: 0.8567 (mpp) cc_final: 0.8275 (mpp) REVERT: D 615 ASN cc_start: 0.8709 (t0) cc_final: 0.8332 (t0) REVERT: D 714 CYS cc_start: 0.9087 (t) cc_final: 0.8614 (m) REVERT: E 81 ASP cc_start: 0.7546 (t0) cc_final: 0.7226 (t0) REVERT: F 24 MET cc_start: 0.8754 (tpt) cc_final: 0.8046 (tpt) REVERT: F 58 MET cc_start: 0.8215 (mmm) cc_final: 0.7984 (tpp) REVERT: F 81 ASP cc_start: 0.8548 (t0) cc_final: 0.8330 (t0) REVERT: G 58 MET cc_start: 0.7829 (tpp) cc_final: 0.7567 (tpp) REVERT: G 70 GLU cc_start: 0.7784 (mp0) cc_final: 0.7445 (mp0) REVERT: G 206 GLN cc_start: 0.9218 (pt0) cc_final: 0.8933 (pp30) REVERT: H 81 ASP cc_start: 0.7979 (t0) cc_final: 0.7549 (t0) outliers start: 53 outliers final: 23 residues processed: 232 average time/residue: 0.1129 time to fit residues: 42.1627 Evaluate side-chains 187 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 138 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 191 optimal weight: 0.0870 chunk 184 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 134 optimal weight: 0.1980 chunk 211 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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** E 204 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS G 60 HIS ** 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 = 0.4275 r_free = 0.4275 target = 0.104080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.075878 restraints weight = 232194.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.078540 restraints weight = 95582.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.080455 restraints weight = 55155.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.081765 restraints weight = 38193.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.082637 restraints weight = 29233.079| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17289 Z= 0.115 Angle : 0.566 8.546 23479 Z= 0.290 Chirality : 0.040 0.227 2712 Planarity : 0.004 0.043 2882 Dihedral : 4.328 52.868 2423 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.43 % Favored : 98.34 % Rotamer: Outliers : 2.50 % Allowed : 19.89 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.18), residues: 2185 helix: 2.49 (0.14), residues: 1331 sheet: -1.83 (0.36), residues: 162 loop : -0.55 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 416 TYR 0.016 0.001 TYR C 728 PHE 0.023 0.001 PHE C 655 TRP 0.019 0.001 TRP A 601 HIS 0.019 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00243 (17281) covalent geometry : angle 0.56496 (23463) SS BOND : bond 0.00547 ( 8) SS BOND : angle 1.30004 ( 16) hydrogen bonds : bond 0.03674 ( 1107) hydrogen bonds : angle 3.85784 ( 3230) *********************** 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 230 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 LEU cc_start: 0.9388 (tp) cc_final: 0.9135 (tt) REVERT: A 581 MET cc_start: 0.8150 (mpp) cc_final: 0.7799 (mpp) REVERT: B 581 MET cc_start: 0.8952 (mmp) cc_final: 0.8545 (mmt) REVERT: C 403 MET cc_start: 0.3229 (mpp) cc_final: 0.2950 (mpp) REVERT: C 500 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6479 (mm) REVERT: C 605 THR cc_start: 0.8863 (m) cc_final: 0.8493 (m) REVERT: C 704 MET cc_start: 0.8438 (mpp) cc_final: 0.8078 (mpp) REVERT: D 615 ASN cc_start: 0.8817 (t0) cc_final: 0.8383 (t0) REVERT: D 704 MET cc_start: 0.7604 (ptp) cc_final: 0.7318 (mpp) REVERT: D 714 CYS cc_start: 0.8757 (t) cc_final: 0.8286 (m) REVERT: E 81 ASP cc_start: 0.7529 (t0) cc_final: 0.7176 (t0) REVERT: E 153 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9224 (mp) REVERT: F 24 MET cc_start: 0.8602 (tpt) cc_final: 0.7948 (tpt) REVERT: F 58 MET cc_start: 0.8221 (mmm) cc_final: 0.8017 (tpp) REVERT: F 81 ASP cc_start: 0.8455 (t0) cc_final: 0.8238 (t0) REVERT: G 33 TRP cc_start: 0.8093 (m-10) cc_final: 0.7689 (m100) REVERT: G 58 MET cc_start: 0.8224 (tpp) cc_final: 0.7938 (tpp) REVERT: G 190 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8188 (mm-30) REVERT: H 81 ASP cc_start: 0.7864 (t0) cc_final: 0.7379 (t0) REVERT: H 113 THR cc_start: 0.9399 (m) cc_final: 0.9180 (p) outliers start: 40 outliers final: 22 residues processed: 219 average time/residue: 0.1154 time to fit residues: 41.3301 Evaluate side-chains 195 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 475 LEU 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 801 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR 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 807 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 153 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 H residue 122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 61 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.099045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.070850 restraints weight = 237996.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.073350 restraints weight = 102013.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.075108 restraints weight = 59674.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.076310 restraints weight = 41738.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.077018 restraints weight = 33012.670| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17289 Z= 0.184 Angle : 0.609 9.040 23479 Z= 0.317 Chirality : 0.041 0.176 2712 Planarity : 0.004 0.048 2882 Dihedral : 4.304 52.062 2419 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.48 % Favored : 98.29 % Rotamer: Outliers : 3.39 % Allowed : 20.49 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.18), residues: 2185 helix: 2.39 (0.14), residues: 1333 sheet: -1.53 (0.38), residues: 161 loop : -0.32 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 208 TYR 0.017 0.001 TYR C 728 PHE 0.019 0.001 PHE B 491 TRP 0.023 0.002 TRP A 601 HIS 0.024 0.002 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00403 (17281) covalent geometry : angle 0.60821 (23463) SS BOND : bond 0.00396 ( 8) SS BOND : angle 1.09633 ( 16) hydrogen bonds : bond 0.03970 ( 1107) hydrogen bonds : angle 4.05410 ( 3230) *********************** 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 222 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 0.677 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 581 MET cc_start: 0.8445 (mpp) cc_final: 0.7914 (mpp) REVERT: B 581 MET cc_start: 0.9174 (mmp) cc_final: 0.8806 (mmm) REVERT: C 403 MET cc_start: 0.3440 (mpp) cc_final: 0.3177 (mpp) REVERT: C 500 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6787 (mm) REVERT: C 605 THR cc_start: 0.8961 (m) cc_final: 0.8568 (m) REVERT: C 686 MET cc_start: 0.8528 (ppp) cc_final: 0.8285 (ppp) REVERT: C 704 MET cc_start: 0.8589 (mpp) cc_final: 0.8191 (mpp) REVERT: C 734 LYS cc_start: 0.6992 (pttm) cc_final: 0.6777 (mttt) REVERT: D 615 ASN cc_start: 0.8810 (t0) cc_final: 0.8389 (t0) REVERT: D 714 CYS cc_start: 0.8781 (t) cc_final: 0.8259 (m) REVERT: E 81 ASP cc_start: 0.7541 (t0) cc_final: 0.7217 (t0) REVERT: E 190 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8488 (tm-30) REVERT: F 58 MET cc_start: 0.8342 (mmm) cc_final: 0.8095 (tpp) REVERT: F 81 ASP cc_start: 0.8350 (t0) cc_final: 0.8064 (t0) REVERT: G 190 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8319 (mm-30) REVERT: G 204 HIS cc_start: 0.5941 (OUTLIER) cc_final: 0.5681 (m-70) REVERT: H 81 ASP cc_start: 0.8004 (t0) cc_final: 0.7558 (t0) REVERT: H 113 THR cc_start: 0.9422 (m) cc_final: 0.9204 (p) REVERT: H 190 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8038 (tm-30) outliers start: 57 outliers final: 35 residues processed: 205 average time/residue: 0.1107 time to fit residues: 37.4151 Evaluate side-chains 191 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 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 533 SER Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 207 LEU 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 11 LEU Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 106 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 157 ILE Chi-restraints excluded: chain H residue 190 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 50 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 150 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 638 GLN ** B 710 GLN ** 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** F 198 HIS G 160 ASN G 204 HIS G 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.094667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.066802 restraints weight = 247370.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.069079 restraints weight = 105311.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.070677 restraints weight = 60889.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.071646 restraints weight = 42844.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.072505 restraints weight = 34545.508| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17289 Z= 0.254 Angle : 0.690 9.789 23479 Z= 0.361 Chirality : 0.043 0.239 2712 Planarity : 0.004 0.067 2882 Dihedral : 4.489 49.560 2416 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.03 % Favored : 97.78 % Rotamer: Outliers : 4.65 % Allowed : 20.96 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.18), residues: 2185 helix: 1.87 (0.14), residues: 1334 sheet: -1.83 (0.39), residues: 150 loop : -0.38 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 37 TYR 0.022 0.002 TYR B 728 PHE 0.019 0.002 PHE B 580 TRP 0.024 0.002 TRP A 601 HIS 0.010 0.002 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00555 (17281) covalent geometry : angle 0.68995 (23463) SS BOND : bond 0.00297 ( 8) SS BOND : angle 1.17276 ( 16) hydrogen bonds : bond 0.04402 ( 1107) hydrogen bonds : angle 4.49656 ( 3230) *********************** 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 228 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 152 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.6500 (mpp) cc_final: 0.6144 (mpp) REVERT: A 511 PHE cc_start: 0.5072 (OUTLIER) cc_final: 0.4052 (p90) REVERT: A 581 MET cc_start: 0.8442 (mpp) cc_final: 0.8041 (mpp) REVERT: B 581 MET cc_start: 0.9019 (mmp) cc_final: 0.8772 (mmm) REVERT: C 403 MET cc_start: 0.3580 (mpp) cc_final: 0.3017 (mpp) REVERT: C 523 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8296 (ttm) REVERT: C 583 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8611 (tp40) REVERT: C 605 THR cc_start: 0.9007 (m) cc_final: 0.8656 (m) REVERT: C 686 MET cc_start: 0.8741 (ppp) cc_final: 0.8448 (ppp) REVERT: C 704 MET cc_start: 0.8664 (mpp) cc_final: 0.8207 (mpp) REVERT: C 717 MET cc_start: 0.7978 (ptt) cc_final: 0.7365 (mmt) REVERT: D 615 ASN cc_start: 0.8768 (t0) cc_final: 0.8409 (t0) REVERT: D 743 ASN cc_start: 0.3523 (OUTLIER) cc_final: 0.3260 (m-40) REVERT: E 56 GLU cc_start: 0.8336 (pm20) cc_final: 0.8099 (tm-30) REVERT: E 81 ASP cc_start: 0.7507 (t0) cc_final: 0.7177 (t0) REVERT: E 190 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8560 (tm-30) REVERT: F 24 MET cc_start: 0.9204 (tpt) cc_final: 0.8183 (tpt) REVERT: F 204 HIS cc_start: 0.6123 (OUTLIER) cc_final: 0.5884 (m170) REVERT: G 190 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8497 (mm-30) REVERT: H 10 MET cc_start: 0.8704 (ppp) cc_final: 0.8362 (ppp) REVERT: H 81 ASP cc_start: 0.7935 (t0) cc_final: 0.7528 (t0) REVERT: H 113 THR cc_start: 0.9436 (m) cc_final: 0.9203 (p) REVERT: H 147 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9322 (mp) REVERT: H 204 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7592 (m-70) outliers start: 76 outliers final: 47 residues processed: 211 average time/residue: 0.1111 time to fit residues: 38.8856 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 : 0.724 ------------------------------------------------------------------------------- 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 492 MET 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 475 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 523 MET 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 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 494 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 587 ILE 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 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 113 THR 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 204 HIS Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 157 ILE 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 55 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.098689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.070932 restraints weight = 248468.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.073383 restraints weight = 104150.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.075117 restraints weight = 59880.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.075660 restraints weight = 41992.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.076842 restraints weight = 35382.320| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17289 Z= 0.124 Angle : 0.590 9.114 23479 Z= 0.297 Chirality : 0.041 0.232 2712 Planarity : 0.004 0.050 2882 Dihedral : 4.126 49.306 2416 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.94 % Favored : 97.92 % Rotamer: Outliers : 3.69 % Allowed : 22.28 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.18), residues: 2185 helix: 2.23 (0.14), residues: 1333 sheet: -1.79 (0.41), residues: 141 loop : -0.35 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 37 TYR 0.019 0.001 TYR B 728 PHE 0.011 0.001 PHE D 542 TRP 0.026 0.001 TRP A 601 HIS 0.007 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00273 (17281) covalent geometry : angle 0.59017 (23463) SS BOND : bond 0.00275 ( 8) SS BOND : angle 0.78081 ( 16) hydrogen bonds : bond 0.03648 ( 1107) hydrogen bonds : angle 4.03359 ( 3230) *********************** 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 225 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 0.654 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: 0.5420 (OUTLIER) cc_final: 0.3727 (p90) REVERT: A 538 LEU cc_start: 0.9377 (tp) cc_final: 0.9138 (tt) REVERT: A 581 MET cc_start: 0.8424 (mpp) cc_final: 0.7951 (mpp) REVERT: B 403 MET cc_start: 0.7586 (pmm) cc_final: 0.6846 (pmm) REVERT: B 538 LEU cc_start: 0.9161 (tt) cc_final: 0.8930 (tp) REVERT: B 686 MET cc_start: 0.8605 (tpp) cc_final: 0.8333 (tpp) REVERT: C 403 MET cc_start: 0.3813 (mpp) cc_final: 0.3424 (mpp) REVERT: C 500 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6647 (mm) REVERT: C 583 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8334 (tp40) REVERT: C 686 MET cc_start: 0.8890 (ppp) cc_final: 0.8600 (ppp) REVERT: D 615 ASN cc_start: 0.8780 (t0) cc_final: 0.8427 (t0) REVERT: D 714 CYS cc_start: 0.8801 (t) cc_final: 0.8260 (m) REVERT: E 81 ASP cc_start: 0.7650 (t0) cc_final: 0.7358 (t0) REVERT: E 153 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9216 (mp) REVERT: F 58 MET cc_start: 0.8329 (tpp) cc_final: 0.7784 (tpp) REVERT: F 81 ASP cc_start: 0.8258 (t0) cc_final: 0.8053 (t0) REVERT: G 190 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8483 (mm-30) REVERT: G 204 HIS cc_start: 0.5673 (OUTLIER) cc_final: 0.4783 (m90) REVERT: H 10 MET cc_start: 0.8779 (ppp) cc_final: 0.8543 (ppp) REVERT: H 34 LEU cc_start: 0.8671 (tp) cc_final: 0.8447 (tp) REVERT: H 81 ASP cc_start: 0.7842 (t0) cc_final: 0.7565 (t0) REVERT: H 113 THR cc_start: 0.9423 (m) cc_final: 0.9202 (p) REVERT: H 147 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9397 (mt) REVERT: H 181 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: H 190 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7917 (tm-30) outliers start: 60 outliers final: 32 residues processed: 213 average time/residue: 0.1099 time to fit residues: 38.7980 Evaluate side-chains 192 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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 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 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 523 MET 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 799 LEU 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 807 LEU 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 61 SER Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 117 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 110 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 174 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** C 583 GLN ** 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 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.097734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.070845 restraints weight = 203526.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.073830 restraints weight = 96787.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.076149 restraints weight = 53380.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.075987 restraints weight = 39166.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.076148 restraints weight = 33388.040| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17289 Z= 0.149 Angle : 0.626 10.896 23479 Z= 0.315 Chirality : 0.041 0.212 2712 Planarity : 0.004 0.051 2882 Dihedral : 4.111 47.495 2416 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.75 % Favored : 98.11 % Rotamer: Outliers : 3.69 % Allowed : 22.63 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.18), residues: 2185 helix: 2.19 (0.14), residues: 1340 sheet: -1.59 (0.43), residues: 134 loop : -0.31 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 37 TYR 0.025 0.001 TYR B 643 PHE 0.015 0.001 PHE C 580 TRP 0.038 0.001 TRP A 601 HIS 0.003 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00333 (17281) covalent geometry : angle 0.62531 (23463) SS BOND : bond 0.00341 ( 8) SS BOND : angle 0.95244 ( 16) hydrogen bonds : bond 0.03680 ( 1107) hydrogen bonds : angle 4.07036 ( 3230) *********************** 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 219 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.732 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: 0.6453 (mpp) cc_final: 0.5769 (mpp) REVERT: A 511 PHE cc_start: 0.5532 (OUTLIER) cc_final: 0.3787 (p90) REVERT: A 538 LEU cc_start: 0.9378 (tp) cc_final: 0.9148 (tt) REVERT: A 604 PHE cc_start: 0.8926 (t80) cc_final: 0.8662 (t80) REVERT: B 403 MET cc_start: 0.7702 (pmm) cc_final: 0.7048 (pmm) REVERT: B 686 MET cc_start: 0.8590 (tpp) cc_final: 0.8314 (tpp) REVERT: C 403 MET cc_start: 0.4073 (mpp) cc_final: 0.3536 (mpp) REVERT: C 686 MET cc_start: 0.8872 (ppp) cc_final: 0.8563 (ppp) REVERT: C 704 MET cc_start: 0.8345 (mpp) cc_final: 0.7760 (mpp) REVERT: C 717 MET cc_start: 0.7923 (ptt) cc_final: 0.7224 (mmp) REVERT: D 499 MET cc_start: 0.2444 (tmm) cc_final: 0.2116 (ppp) REVERT: D 615 ASN cc_start: 0.8697 (t0) cc_final: 0.8327 (t0) REVERT: D 714 CYS cc_start: 0.8657 (t) cc_final: 0.8111 (m) REVERT: E 81 ASP cc_start: 0.7662 (t0) cc_final: 0.7371 (t0) REVERT: E 153 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9202 (mp) REVERT: F 24 MET cc_start: 0.9039 (tpt) cc_final: 0.8260 (tpt) REVERT: F 58 MET cc_start: 0.8338 (tpp) cc_final: 0.7819 (tpp) REVERT: G 190 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8412 (mm-30) REVERT: G 204 HIS cc_start: 0.5697 (OUTLIER) cc_final: 0.4660 (m90) REVERT: H 10 MET cc_start: 0.8780 (ppp) cc_final: 0.8553 (ppp) REVERT: H 34 LEU cc_start: 0.8733 (tp) cc_final: 0.8524 (tp) REVERT: H 81 ASP cc_start: 0.7919 (t0) cc_final: 0.7649 (t0) REVERT: H 113 THR cc_start: 0.9407 (m) cc_final: 0.9175 (p) REVERT: H 147 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9405 (mt) REVERT: H 181 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8076 (m-80) outliers start: 60 outliers final: 41 residues processed: 205 average time/residue: 0.1116 time to fit residues: 38.0570 Evaluate side-chains 195 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 510 VAL Chi-restraints excluded: chain A residue 511 PHE Chi-restraints excluded: chain A residue 526 VAL 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 393 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 397 LEU 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 807 LEU Chi-restraints excluded: chain E residue 11 LEU 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 61 SER Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 77 CYS 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 G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 95 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 177 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 22 optimal weight: 30.0000 chunk 172 optimal weight: 20.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- 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** ** G 206 GLN ** 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 = 0.4150 r_free = 0.4150 target = 0.093696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.066614 restraints weight = 216186.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.068767 restraints weight = 98372.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.070298 restraints weight = 58026.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.070875 restraints weight = 41725.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.071997 restraints weight = 33688.362| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4577 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= 0.220 Angle : 0.696 14.324 23479 Z= 0.355 Chirality : 0.043 0.191 2712 Planarity : 0.004 0.049 2882 Dihedral : 4.405 44.263 2416 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.40 % Favored : 97.46 % Rotamer: Outliers : 3.57 % Allowed : 22.75 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.18), residues: 2185 helix: 1.91 (0.14), residues: 1335 sheet: -1.61 (0.43), residues: 135 loop : -0.34 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 541 TYR 0.022 0.002 TYR B 728 PHE 0.021 0.001 PHE C 580 TRP 0.035 0.002 TRP A 601 HIS 0.004 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00485 (17281) covalent geometry : angle 0.69599 (23463) SS BOND : bond 0.00261 ( 8) SS BOND : angle 1.11751 ( 16) hydrogen bonds : bond 0.04220 ( 1107) hydrogen bonds : angle 4.40050 ( 3230) *********************** 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 200 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 142 time to evaluate : 0.668 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: 0.5166 (OUTLIER) cc_final: 0.4115 (p90) REVERT: B 686 MET cc_start: 0.8760 (tpp) cc_final: 0.8536 (tpp) REVERT: C 403 MET cc_start: 0.4296 (mpp) cc_final: 0.3862 (mpp) REVERT: C 686 MET cc_start: 0.8967 (ppp) cc_final: 0.8662 (ppp) REVERT: C 704 MET cc_start: 0.8444 (mpp) cc_final: 0.7847 (mpp) REVERT: D 499 MET cc_start: 0.2888 (tmm) cc_final: 0.2563 (ppp) REVERT: D 615 ASN cc_start: 0.8771 (t0) cc_final: 0.8367 (t0) REVERT: E 81 ASP cc_start: 0.7578 (t0) cc_final: 0.7291 (t0) REVERT: F 58 MET cc_start: 0.8372 (tpp) cc_final: 0.7825 (tpp) REVERT: G 190 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8436 (mm-30) REVERT: G 204 HIS cc_start: 0.6137 (OUTLIER) cc_final: 0.5056 (m90) REVERT: H 10 MET cc_start: 0.8758 (ppp) cc_final: 0.8536 (ppp) REVERT: H 81 ASP cc_start: 0.8146 (t0) cc_final: 0.7914 (t0) REVERT: H 113 THR cc_start: 0.9470 (m) cc_final: 0.9238 (p) REVERT: H 147 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9419 (mp) REVERT: H 181 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8045 (m-80) outliers start: 58 outliers final: 43 residues processed: 187 average time/residue: 0.1078 time to fit residues: 33.9120 Evaluate side-chains 188 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 732 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 500 ILE 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 799 LEU 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 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 77 CYS 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 G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 126 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 148 optimal weight: 0.4980 chunk 121 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 82 HIS F 160 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.099162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.071861 restraints weight = 265454.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.074437 restraints weight = 109842.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.076171 restraints weight = 61969.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.077358 restraints weight = 42600.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.078175 restraints weight = 33300.674| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17289 Z= 0.121 Angle : 0.636 12.031 23479 Z= 0.314 Chirality : 0.041 0.186 2712 Planarity : 0.004 0.048 2882 Dihedral : 3.956 46.014 2414 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.57 % Favored : 98.29 % Rotamer: Outliers : 2.38 % Allowed : 24.00 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.18), residues: 2185 helix: 2.21 (0.14), residues: 1328 sheet: -1.35 (0.45), residues: 136 loop : -0.37 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 37 TYR 0.018 0.001 TYR B 728 PHE 0.018 0.001 PHE C 580 TRP 0.047 0.001 TRP A 601 HIS 0.005 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00264 (17281) covalent geometry : angle 0.63569 (23463) SS BOND : bond 0.00283 ( 8) SS BOND : angle 0.80711 ( 16) hydrogen bonds : bond 0.03530 ( 1107) hydrogen bonds : angle 3.99066 ( 3230) *********************** 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 204 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 LEU cc_start: 0.9347 (tp) cc_final: 0.9109 (tt) REVERT: B 686 MET cc_start: 0.8628 (tpp) cc_final: 0.8368 (tpp) REVERT: C 605 THR cc_start: 0.8756 (m) cc_final: 0.8528 (m) REVERT: C 637 LYS cc_start: 0.8012 (tmmt) cc_final: 0.7808 (ptmm) REVERT: C 704 MET cc_start: 0.8342 (mpp) cc_final: 0.7758 (mpp) REVERT: C 717 MET cc_start: 0.7834 (ptt) cc_final: 0.7280 (mmp) REVERT: C 734 LYS cc_start: 0.7456 (mttt) cc_final: 0.7012 (mmmt) REVERT: D 499 MET cc_start: 0.2197 (tmm) cc_final: 0.1937 (ppp) REVERT: D 615 ASN cc_start: 0.8724 (t0) cc_final: 0.8371 (t0) REVERT: D 714 CYS cc_start: 0.8837 (t) cc_final: 0.8336 (m) REVERT: E 56 GLU cc_start: 0.8492 (pm20) cc_final: 0.8207 (mm-30) REVERT: E 81 ASP cc_start: 0.7348 (t0) cc_final: 0.7087 (t0) REVERT: E 190 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8582 (tm-30) REVERT: F 24 MET cc_start: 0.9011 (tpt) cc_final: 0.8568 (tpt) REVERT: F 58 MET cc_start: 0.8275 (tpp) cc_final: 0.7849 (tpp) REVERT: G 190 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8488 (mm-30) REVERT: G 204 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.4959 (m90) REVERT: H 10 MET cc_start: 0.8753 (ppp) cc_final: 0.8525 (ppp) REVERT: H 34 LEU cc_start: 0.8597 (tp) cc_final: 0.8359 (tp) REVERT: H 113 THR cc_start: 0.9452 (m) cc_final: 0.9225 (p) REVERT: H 147 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9387 (mt) REVERT: H 181 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7912 (m-80) outliers start: 38 outliers final: 30 residues processed: 193 average time/residue: 0.1088 time to fit residues: 34.9752 Evaluate side-chains 188 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 576 SER Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 650 SER 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 B residue 704 MET Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 629 ILE 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 E residue 66 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 G residue 67 CYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 218 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 198 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.098738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.071556 restraints weight = 247540.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.073921 restraints weight = 104496.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.075737 restraints weight = 60249.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.076222 restraints weight = 41732.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.077539 restraints weight = 35278.057| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4674 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= 0.128 Angle : 0.667 14.374 23479 Z= 0.328 Chirality : 0.041 0.192 2712 Planarity : 0.004 0.048 2882 Dihedral : 3.993 49.153 2414 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.80 % Favored : 98.06 % Rotamer: Outliers : 2.08 % Allowed : 24.30 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.18), residues: 2185 helix: 2.11 (0.14), residues: 1340 sheet: -1.39 (0.46), residues: 121 loop : -0.32 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 37 TYR 0.016 0.001 TYR B 728 PHE 0.021 0.001 PHE C 580 TRP 0.077 0.001 TRP A 601 HIS 0.004 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00286 (17281) covalent geometry : angle 0.66688 (23463) SS BOND : bond 0.00259 ( 8) SS BOND : angle 0.81235 ( 16) hydrogen bonds : bond 0.03515 ( 1107) hydrogen bonds : angle 4.00140 ( 3230) ********************** 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 190 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 LEU cc_start: 0.9340 (tp) cc_final: 0.9097 (tt) REVERT: B 686 MET cc_start: 0.8610 (tpp) cc_final: 0.8335 (tpp) REVERT: C 500 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7519 (mm) REVERT: C 704 MET cc_start: 0.8380 (mpp) cc_final: 0.7912 (mpp) REVERT: C 717 MET cc_start: 0.7907 (ptt) cc_final: 0.7334 (mmp) REVERT: C 734 LYS cc_start: 0.7642 (mttt) cc_final: 0.7184 (mmmt) REVERT: D 499 MET cc_start: 0.1995 (tmm) cc_final: 0.1770 (ppp) REVERT: D 615 ASN cc_start: 0.8724 (t0) cc_final: 0.8327 (t0) REVERT: D 714 CYS cc_start: 0.8800 (t) cc_final: 0.8290 (m) REVERT: E 56 GLU cc_start: 0.8577 (pm20) cc_final: 0.8190 (mm-30) REVERT: E 81 ASP cc_start: 0.7369 (t0) cc_final: 0.7106 (t0) REVERT: F 24 MET cc_start: 0.8875 (tpt) cc_final: 0.8433 (tpt) REVERT: F 58 MET cc_start: 0.8284 (tpp) cc_final: 0.7863 (tpp) REVERT: G 136 LEU cc_start: 0.9108 (mt) cc_final: 0.8809 (pp) REVERT: G 190 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8494 (mm-30) REVERT: G 204 HIS cc_start: 0.5891 (OUTLIER) cc_final: 0.4865 (m90) REVERT: H 10 MET cc_start: 0.8797 (ppp) cc_final: 0.8565 (ppp) REVERT: H 113 THR cc_start: 0.9464 (m) cc_final: 0.9230 (p) REVERT: H 181 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7907 (m-80) outliers start: 33 outliers final: 26 residues processed: 181 average time/residue: 0.1054 time to fit residues: 31.5842 Evaluate side-chains 183 residues out of total 1851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 576 SER Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 629 ILE 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 E residue 66 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 G residue 67 CYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 181 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 192 optimal weight: 30.0000 chunk 162 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 198 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.098526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.071116 restraints weight = 270966.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.073681 restraints weight = 110053.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.075411 restraints weight = 62330.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.076711 restraints weight = 43499.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.077517 restraints weight = 33702.849| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17289 Z= 0.130 Angle : 0.653 12.463 23479 Z= 0.321 Chirality : 0.041 0.209 2712 Planarity : 0.004 0.048 2882 Dihedral : 3.940 52.743 2414 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.75 % Favored : 98.11 % Rotamer: Outliers : 2.32 % Allowed : 23.76 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.18), residues: 2185 helix: 2.16 (0.14), residues: 1338 sheet: -1.52 (0.49), residues: 111 loop : -0.32 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 37 TYR 0.019 0.001 TYR H 173 PHE 0.030 0.001 PHE C 580 TRP 0.078 0.002 TRP A 601 HIS 0.004 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00296 (17281) covalent geometry : angle 0.65266 (23463) SS BOND : bond 0.00252 ( 8) SS BOND : angle 0.80115 ( 16) hydrogen bonds : bond 0.03505 ( 1107) hydrogen bonds : angle 3.96550 ( 3230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3897.80 seconds wall clock time: 67 minutes 53.77 seconds (4073.77 seconds total)