Starting phenix.real_space_refine on Sat Jun 14 18:30:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v7o_43008/06_2025/8v7o_43008_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v7o_43008/06_2025/8v7o_43008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v7o_43008/06_2025/8v7o_43008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v7o_43008/06_2025/8v7o_43008.map" model { file = "/net/cci-nas-00/data/ceres_data/8v7o_43008/06_2025/8v7o_43008_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v7o_43008/06_2025/8v7o_43008_neut.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 69 5.16 5 C 10401 2.51 5 N 2829 2.21 5 O 3153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 198 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16452 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3771 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3771 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3771 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 928 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 928 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "J" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 928 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 785 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "M" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 785 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "N" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 785 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 99} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 11.97, per 1000 atoms: 0.73 Number of scatterers: 16452 At special positions: 0 Unit cell: (117.298, 117.824, 178.314, 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 69 16.00 O 3153 8.00 N 2829 7.00 C 10401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.02 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 463 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.02 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.02 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 302 " distance=2.02 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 45 sheets defined 18.5% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 183 through 192 Processing helix chain 'A' and resid 364 through 384 Processing helix chain 'A' and resid 400 through 451 removed outlier: 3.966A pdb=" N GLU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN A 451 " --> pdb=" O LYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.879A pdb=" N TYR A 488 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 489 " --> pdb=" O PRO A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 489' Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 183 through 192 Processing helix chain 'B' and resid 364 through 384 Processing helix chain 'B' and resid 400 through 451 removed outlier: 3.966A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 485 through 489 removed outlier: 3.880A pdb=" N TYR B 488 " --> pdb=" O TYR B 485 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 485 through 489' Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 364 through 384 Processing helix chain 'C' and resid 400 through 451 removed outlier: 3.966A pdb=" N GLU C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN C 451 " --> pdb=" O LYS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 481 Processing helix chain 'C' and resid 485 through 489 removed outlier: 3.880A pdb=" N TYR C 488 " --> pdb=" O TYR C 485 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 489 " --> pdb=" O PRO C 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 485 through 489' Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'I' and resid 69 through 72 Processing helix chain 'J' and resid 69 through 72 Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'N' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 353 removed outlier: 3.708A pdb=" N GLY A 349 " --> pdb=" O GLY A 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 6 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A 4 " --> pdb=" O HIS A 351 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 3 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 18 removed outlier: 4.063A pdb=" N ASP A 14 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 18 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 115 removed outlier: 6.953A pdb=" N TYR A 252 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A 175 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 227 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 137 removed outlier: 4.667A pdb=" N CYS A 135 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 142 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA7, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA8, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.522A pdb=" N VAL A 200 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 278 through 280 removed outlier: 4.104A pdb=" N CYS A 278 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 353 removed outlier: 3.708A pdb=" N GLY B 349 " --> pdb=" O GLY B 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 6 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS B 4 " --> pdb=" O HIS B 351 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 3 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 14 through 18 removed outlier: 4.063A pdb=" N ASP B 14 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR B 18 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AB4, first strand: chain 'B' and resid 112 through 115 removed outlier: 6.952A pdb=" N TYR B 252 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU B 175 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 227 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 132 through 137 removed outlier: 4.667A pdb=" N CYS B 135 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 142 " --> pdb=" O CYS B 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 147 through 148 Processing sheet with id=AB7, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AB8, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.522A pdb=" N VAL B 200 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 278 through 280 removed outlier: 4.104A pdb=" N CYS B 278 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 348 through 353 removed outlier: 3.708A pdb=" N GLY C 349 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY C 6 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C 4 " --> pdb=" O HIS C 351 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 3 " --> pdb=" O PHE C 464 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 14 through 18 removed outlier: 4.063A pdb=" N ASP C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 18 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC4, first strand: chain 'C' and resid 112 through 115 removed outlier: 6.952A pdb=" N TYR C 252 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU C 175 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 227 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 132 through 137 removed outlier: 4.668A pdb=" N CYS C 135 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 142 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 147 through 148 Processing sheet with id=AC7, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AC8, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.523A pdb=" N VAL C 200 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 278 through 280 removed outlier: 4.105A pdb=" N CYS C 278 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 4 through 6 removed outlier: 4.201A pdb=" N GLU H 17 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU H 19 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ARG H 92 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU H 21 " --> pdb=" O LYS H 90 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYS H 90 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS H 23 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER H 88 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL H 25 " --> pdb=" O GLN H 86 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN H 86 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER H 88 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER H 79 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR H 77 " --> pdb=" O LYS H 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.115A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP H 41 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR H 113 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.115A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY H 54 " --> pdb=" O TRP H 41 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP H 41 " --> pdb=" O GLY H 54 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 4 through 6 removed outlier: 4.201A pdb=" N GLU I 17 " --> pdb=" O VAL I 94 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU I 19 " --> pdb=" O ARG I 92 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ARG I 92 " --> pdb=" O LEU I 19 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU I 21 " --> pdb=" O LYS I 90 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LYS I 90 " --> pdb=" O LEU I 21 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS I 23 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER I 88 " --> pdb=" O CYS I 23 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL I 25 " --> pdb=" O GLN I 86 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN I 86 " --> pdb=" O VAL I 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER I 88 " --> pdb=" O SER I 79 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER I 79 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR I 77 " --> pdb=" O LYS I 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 65 through 67 removed outlier: 5.115A pdb=" N TRP I 52 " --> pdb=" O ARG I 43 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG I 43 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY I 54 " --> pdb=" O TRP I 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP I 41 " --> pdb=" O GLY I 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR I 113 " --> pdb=" O ASP I 110 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 65 through 67 removed outlier: 5.115A pdb=" N TRP I 52 " --> pdb=" O ARG I 43 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG I 43 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY I 54 " --> pdb=" O TRP I 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP I 41 " --> pdb=" O GLY I 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 4 through 6 removed outlier: 4.201A pdb=" N GLU J 17 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU J 19 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG J 92 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU J 21 " --> pdb=" O LYS J 90 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYS J 90 " --> pdb=" O LEU J 21 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS J 23 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER J 88 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL J 25 " --> pdb=" O GLN J 86 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN J 86 " --> pdb=" O VAL J 25 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER J 88 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER J 79 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR J 77 " --> pdb=" O LYS J 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.114A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY J 54 " --> pdb=" O TRP J 41 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP J 41 " --> pdb=" O GLY J 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR J 113 " --> pdb=" O ASP J 110 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.114A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY J 54 " --> pdb=" O TRP J 41 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP J 41 " --> pdb=" O GLY J 54 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.547A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA L 19 " --> pdb=" O ILE L 91 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AE3, first strand: chain 'L' and resid 66 through 67 removed outlier: 5.485A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.547A pdb=" N SER M 7 " --> pdb=" O SER M 22 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA M 19 " --> pdb=" O ILE M 91 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'M' and resid 66 through 67 removed outlier: 5.486A pdb=" N LEU M 52 " --> pdb=" O GLN M 43 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.547A pdb=" N SER N 7 " --> pdb=" O SER N 22 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA N 19 " --> pdb=" O ILE N 91 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AE9, first strand: chain 'N' and resid 66 through 67 removed outlier: 5.485A pdb=" N LEU N 52 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN N 43 " --> pdb=" O LEU N 52 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.53 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5289 1.34 - 1.46: 3754 1.46 - 1.58: 7736 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 16869 Sorted by residual: bond pdb=" CB TRP I 111A" pdb=" CG TRP I 111A" ideal model delta sigma weight residual 1.498 1.434 0.064 3.10e-02 1.04e+03 4.21e+00 bond pdb=" CD ARG A 401 " pdb=" NE ARG A 401 " ideal model delta sigma weight residual 1.458 1.430 0.028 1.40e-02 5.10e+03 4.14e+00 bond pdb=" CD ARG C 401 " pdb=" NE ARG C 401 " ideal model delta sigma weight residual 1.458 1.430 0.028 1.40e-02 5.10e+03 4.11e+00 bond pdb=" CB TRP J 111A" pdb=" CG TRP J 111A" ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.09e+00 bond pdb=" CB TRP H 111A" pdb=" CG TRP H 111A" ideal model delta sigma weight residual 1.498 1.435 0.063 3.10e-02 1.04e+03 4.07e+00 ... (remaining 16864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 22628 3.23 - 6.45: 315 6.45 - 9.68: 31 9.68 - 12.90: 0 12.90 - 16.13: 6 Bond angle restraints: 22980 Sorted by residual: angle pdb=" N VAL J 111C" pdb=" CA VAL J 111C" pdb=" C VAL J 111C" ideal model delta sigma weight residual 112.29 106.95 5.34 9.40e-01 1.13e+00 3.23e+01 angle pdb=" N VAL H 111C" pdb=" CA VAL H 111C" pdb=" C VAL H 111C" ideal model delta sigma weight residual 112.29 106.97 5.32 9.40e-01 1.13e+00 3.20e+01 angle pdb=" N VAL I 111C" pdb=" CA VAL I 111C" pdb=" C VAL I 111C" ideal model delta sigma weight residual 112.29 106.97 5.32 9.40e-01 1.13e+00 3.20e+01 angle pdb=" CA LEU C 452 " pdb=" CB LEU C 452 " pdb=" CG LEU C 452 " ideal model delta sigma weight residual 116.30 132.43 -16.13 3.50e+00 8.16e-02 2.12e+01 angle pdb=" CA LEU A 452 " pdb=" CB LEU A 452 " pdb=" CG LEU A 452 " ideal model delta sigma weight residual 116.30 132.42 -16.12 3.50e+00 8.16e-02 2.12e+01 ... (remaining 22975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8626 17.95 - 35.90: 1046 35.90 - 53.85: 231 53.85 - 71.80: 36 71.80 - 89.75: 30 Dihedral angle restraints: 9969 sinusoidal: 3777 harmonic: 6192 Sorted by residual: dihedral pdb=" CB CYS C 42 " pdb=" SG CYS C 42 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual -86.00 -14.11 -71.89 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual -86.00 -14.15 -71.85 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS B 42 " pdb=" SG CYS B 42 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual -86.00 -14.15 -71.85 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 9966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1517 0.041 - 0.081: 702 0.081 - 0.122: 229 0.122 - 0.162: 55 0.162 - 0.203: 14 Chirality restraints: 2517 Sorted by residual: chirality pdb=" CA TRP M 110 " pdb=" N TRP M 110 " pdb=" C TRP M 110 " pdb=" CB TRP M 110 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA TRP L 110 " pdb=" N TRP L 110 " pdb=" C TRP L 110 " pdb=" CB TRP L 110 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA TRP N 110 " pdb=" N TRP N 110 " pdb=" C TRP N 110 " pdb=" CB TRP N 110 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2514 not shown) Planarity restraints: 2973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 149 " -0.035 2.00e-02 2.50e+03 2.81e-02 1.98e+01 pdb=" CG TRP B 149 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 149 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 149 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 149 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 149 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 149 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 149 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 149 " -0.035 2.00e-02 2.50e+03 2.81e-02 1.97e+01 pdb=" CG TRP A 149 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP A 149 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 149 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 149 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 149 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 149 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 149 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 149 " -0.035 2.00e-02 2.50e+03 2.80e-02 1.95e+01 pdb=" CG TRP C 149 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP C 149 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 149 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 149 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 149 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 149 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 149 " -0.006 2.00e-02 2.50e+03 ... (remaining 2970 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 470 2.65 - 3.21: 16475 3.21 - 3.77: 24569 3.77 - 4.34: 32499 4.34 - 4.90: 53526 Nonbonded interactions: 127539 Sorted by model distance: nonbonded pdb=" OH TYR L 42 " pdb=" OE1 GLN L 105 " model vdw 2.083 3.040 nonbonded pdb=" OH TYR M 42 " pdb=" OE1 GLN M 105 " model vdw 2.083 3.040 nonbonded pdb=" OH TYR N 42 " pdb=" OE1 GLN N 105 " model vdw 2.083 3.040 nonbonded pdb=" OH TYR B 348 " pdb=" ND1 HIS B 437 " model vdw 2.098 3.120 nonbonded pdb=" OH TYR A 348 " pdb=" ND1 HIS A 437 " model vdw 2.098 3.120 ... (remaining 127534 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: 0.10 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 40.770 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.006 0.068 16893 Z= 0.272 Angle : 0.978 16.126 23028 Z= 0.503 Chirality : 0.052 0.203 2517 Planarity : 0.005 0.063 2973 Dihedral : 16.850 89.754 5943 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.17), residues: 2118 helix: 0.21 (0.27), residues: 336 sheet: -1.87 (0.23), residues: 522 loop : -2.77 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.005 TRP B 149 HIS 0.008 0.002 HIS A 180 PHE 0.023 0.003 PHE N 87 TYR 0.035 0.003 TYR A 305 ARG 0.009 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.24530 ( 540) hydrogen bonds : angle 9.44913 ( 1521) SS BOND : bond 0.00631 ( 24) SS BOND : angle 2.46197 ( 48) covalent geometry : bond 0.00621 (16869) covalent geometry : angle 0.97236 (22980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: 0.6545 (mmm) cc_final: 0.6233 (mmm) REVERT: C 103 GLU cc_start: 0.8476 (tp30) cc_final: 0.8243 (tt0) REVERT: C 343 MET cc_start: 0.6543 (mmm) cc_final: 0.6303 (mmm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2476 time to fit residues: 91.1240 Evaluate side-chains 197 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 0.0020 chunk 85 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 0.1980 chunk 122 optimal weight: 0.0070 chunk 190 optimal weight: 10.0000 overall best weight: 0.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.149014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.117847 restraints weight = 35684.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.120952 restraints weight = 18974.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.122990 restraints weight = 12526.245| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16893 Z= 0.160 Angle : 0.808 13.118 23028 Z= 0.410 Chirality : 0.047 0.163 2517 Planarity : 0.005 0.059 2973 Dihedral : 6.036 22.594 2313 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.06 % Allowed : 11.95 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.18), residues: 2118 helix: 0.90 (0.28), residues: 342 sheet: -1.54 (0.22), residues: 564 loop : -2.55 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 149 HIS 0.008 0.001 HIS C 437 PHE 0.021 0.001 PHE I 112A TYR 0.033 0.002 TYR J 55 ARG 0.006 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 540) hydrogen bonds : angle 6.63347 ( 1521) SS BOND : bond 0.00404 ( 24) SS BOND : angle 1.99418 ( 48) covalent geometry : bond 0.00343 (16869) covalent geometry : angle 0.80338 (22980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 2.057 Fit side-chains REVERT: A 103 GLU cc_start: 0.8473 (tp30) cc_final: 0.8231 (tt0) REVERT: A 403 MET cc_start: 0.8014 (tpp) cc_final: 0.7707 (tpp) REVERT: B 103 GLU cc_start: 0.8468 (tp30) cc_final: 0.8201 (tt0) REVERT: B 343 MET cc_start: 0.6527 (mmm) cc_final: 0.6315 (mmm) REVERT: B 403 MET cc_start: 0.8033 (tpp) cc_final: 0.7787 (tpp) REVERT: C 103 GLU cc_start: 0.8488 (tp30) cc_final: 0.8161 (tt0) REVERT: C 403 MET cc_start: 0.7972 (tpp) cc_final: 0.7717 (tpp) outliers start: 36 outliers final: 30 residues processed: 253 average time/residue: 0.2359 time to fit residues: 96.2792 Evaluate side-chains 235 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 39 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 144 optimal weight: 0.1980 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 0.0270 chunk 66 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.161709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.128419 restraints weight = 37246.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131590 restraints weight = 19412.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133558 restraints weight = 12617.376| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16893 Z= 0.225 Angle : 0.765 10.288 23028 Z= 0.392 Chirality : 0.046 0.156 2517 Planarity : 0.005 0.059 2973 Dihedral : 5.875 21.609 2313 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.32 % Allowed : 17.15 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.18), residues: 2118 helix: 1.10 (0.28), residues: 342 sheet: -1.69 (0.22), residues: 585 loop : -2.54 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 111A HIS 0.007 0.001 HIS B 180 PHE 0.014 0.002 PHE I 112A TYR 0.033 0.002 TYR H 55 ARG 0.004 0.001 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 540) hydrogen bonds : angle 6.12137 ( 1521) SS BOND : bond 0.00500 ( 24) SS BOND : angle 1.81936 ( 48) covalent geometry : bond 0.00517 (16869) covalent geometry : angle 0.76123 (22980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 1.670 Fit side-chains REVERT: A 100 GLU cc_start: 0.8249 (tp30) cc_final: 0.8021 (tp30) REVERT: A 343 MET cc_start: 0.6366 (mmm) cc_final: 0.5916 (tmm) REVERT: A 403 MET cc_start: 0.8051 (tpp) cc_final: 0.7742 (tpp) REVERT: C 403 MET cc_start: 0.7999 (tpp) cc_final: 0.7782 (tpp) REVERT: L 55 TYR cc_start: 0.7395 (p90) cc_final: 0.7085 (p90) outliers start: 58 outliers final: 51 residues processed: 232 average time/residue: 0.2064 time to fit residues: 79.7278 Evaluate side-chains 244 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 39 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 176 optimal weight: 0.2980 chunk 209 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.146928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115581 restraints weight = 35840.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.118675 restraints weight = 18909.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.120698 restraints weight = 12475.975| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16893 Z= 0.158 Angle : 0.697 8.214 23028 Z= 0.359 Chirality : 0.045 0.157 2517 Planarity : 0.004 0.057 2973 Dihedral : 5.601 20.698 2313 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.37 % Allowed : 20.18 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.18), residues: 2118 helix: 1.31 (0.29), residues: 342 sheet: -1.57 (0.22), residues: 582 loop : -2.47 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 41 HIS 0.005 0.001 HIS B 180 PHE 0.012 0.001 PHE A 436 TYR 0.030 0.002 TYR H 55 ARG 0.003 0.001 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 540) hydrogen bonds : angle 5.84083 ( 1521) SS BOND : bond 0.00391 ( 24) SS BOND : angle 1.64651 ( 48) covalent geometry : bond 0.00364 (16869) covalent geometry : angle 0.69394 (22980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 1.721 Fit side-chains REVERT: A 100 GLU cc_start: 0.8227 (tp30) cc_final: 0.7971 (tp30) REVERT: A 343 MET cc_start: 0.6442 (mmm) cc_final: 0.5813 (tmm) REVERT: A 403 MET cc_start: 0.8019 (tpp) cc_final: 0.7791 (tpp) REVERT: B 343 MET cc_start: 0.6431 (mmm) cc_final: 0.6083 (mmm) REVERT: B 403 MET cc_start: 0.8032 (tpp) cc_final: 0.7672 (tpp) REVERT: C 100 GLU cc_start: 0.8260 (tp30) cc_final: 0.8044 (tp30) REVERT: H 99 THR cc_start: 0.8059 (t) cc_final: 0.7818 (t) REVERT: I 99 THR cc_start: 0.7915 (t) cc_final: 0.7704 (t) REVERT: J 99 THR cc_start: 0.7911 (t) cc_final: 0.7667 (t) outliers start: 59 outliers final: 49 residues processed: 246 average time/residue: 0.2274 time to fit residues: 90.8830 Evaluate side-chains 249 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain N residue 39 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 0 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 55 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 443 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS B 443 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS C 443 ASN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.144029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112537 restraints weight = 36783.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.115675 restraints weight = 19202.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.117667 restraints weight = 12550.174| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16893 Z= 0.185 Angle : 0.700 7.621 23028 Z= 0.361 Chirality : 0.045 0.162 2517 Planarity : 0.004 0.054 2973 Dihedral : 5.513 20.573 2313 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.89 % Allowed : 22.41 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.18), residues: 2118 helix: 1.69 (0.29), residues: 321 sheet: -1.52 (0.22), residues: 582 loop : -2.44 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 111A HIS 0.006 0.001 HIS N 66 PHE 0.011 0.002 PHE J 87 TYR 0.031 0.002 TYR H 55 ARG 0.007 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 540) hydrogen bonds : angle 5.72761 ( 1521) SS BOND : bond 0.00450 ( 24) SS BOND : angle 1.60169 ( 48) covalent geometry : bond 0.00425 (16869) covalent geometry : angle 0.69653 (22980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 1.815 Fit side-chains REVERT: A 100 GLU cc_start: 0.8264 (tp30) cc_final: 0.8024 (tp30) REVERT: A 343 MET cc_start: 0.6546 (mmm) cc_final: 0.6012 (mmm) REVERT: A 403 MET cc_start: 0.8001 (tpp) cc_final: 0.7742 (tpp) REVERT: B 403 MET cc_start: 0.8019 (tpp) cc_final: 0.7768 (tpp) REVERT: C 100 GLU cc_start: 0.8264 (tp30) cc_final: 0.8032 (tp30) REVERT: H 99 THR cc_start: 0.8044 (t) cc_final: 0.7817 (t) REVERT: I 99 THR cc_start: 0.7900 (t) cc_final: 0.7695 (t) REVERT: J 99 THR cc_start: 0.7904 (t) cc_final: 0.7667 (t) outliers start: 68 outliers final: 57 residues processed: 243 average time/residue: 0.2392 time to fit residues: 97.8121 Evaluate side-chains 250 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain M residue 39 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 0.0370 chunk 113 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 192 optimal weight: 6.9990 overall best weight: 1.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.142169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110293 restraints weight = 35804.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.113416 restraints weight = 18839.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.115358 restraints weight = 12383.713| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16893 Z= 0.181 Angle : 0.684 7.186 23028 Z= 0.355 Chirality : 0.045 0.170 2517 Planarity : 0.004 0.053 2973 Dihedral : 5.436 20.342 2313 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.54 % Allowed : 23.73 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.18), residues: 2118 helix: 1.59 (0.29), residues: 324 sheet: -1.50 (0.22), residues: 576 loop : -2.39 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 118 HIS 0.006 0.001 HIS N 66 PHE 0.013 0.002 PHE A 436 TYR 0.031 0.002 TYR I 55 ARG 0.004 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 540) hydrogen bonds : angle 5.68247 ( 1521) SS BOND : bond 0.00451 ( 24) SS BOND : angle 1.57786 ( 48) covalent geometry : bond 0.00418 (16869) covalent geometry : angle 0.68130 (22980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 1.899 Fit side-chains REVERT: A 100 GLU cc_start: 0.8345 (tp30) cc_final: 0.8097 (tp30) REVERT: A 343 MET cc_start: 0.6553 (mmm) cc_final: 0.6256 (mmm) REVERT: A 403 MET cc_start: 0.7986 (tpp) cc_final: 0.7728 (tpp) REVERT: B 403 MET cc_start: 0.8025 (tpp) cc_final: 0.7723 (tpp) REVERT: C 100 GLU cc_start: 0.8342 (tp30) cc_final: 0.8095 (tp30) REVERT: H 99 THR cc_start: 0.7916 (t) cc_final: 0.7698 (t) REVERT: J 99 THR cc_start: 0.7831 (t) cc_final: 0.7612 (t) outliers start: 62 outliers final: 55 residues processed: 229 average time/residue: 0.2401 time to fit residues: 93.0853 Evaluate side-chains 243 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 184 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 143 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.142124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.110296 restraints weight = 35856.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.113412 restraints weight = 18799.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.115451 restraints weight = 12367.841| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16893 Z= 0.168 Angle : 0.685 11.134 23028 Z= 0.352 Chirality : 0.045 0.154 2517 Planarity : 0.004 0.052 2973 Dihedral : 5.338 20.289 2313 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.89 % Allowed : 24.07 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.18), residues: 2118 helix: 1.69 (0.29), residues: 324 sheet: -1.48 (0.22), residues: 576 loop : -2.36 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 118 HIS 0.009 0.001 HIS N 66 PHE 0.010 0.001 PHE H 87 TYR 0.030 0.002 TYR I 55 ARG 0.004 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 540) hydrogen bonds : angle 5.60667 ( 1521) SS BOND : bond 0.00430 ( 24) SS BOND : angle 1.53893 ( 48) covalent geometry : bond 0.00387 (16869) covalent geometry : angle 0.68249 (22980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 2.082 Fit side-chains REVERT: A 100 GLU cc_start: 0.8299 (tp30) cc_final: 0.8071 (tp30) REVERT: A 343 MET cc_start: 0.6571 (mmm) cc_final: 0.5825 (tmm) REVERT: A 403 MET cc_start: 0.7974 (tpp) cc_final: 0.7746 (tpp) REVERT: B 403 MET cc_start: 0.8038 (tpp) cc_final: 0.7735 (tpp) REVERT: C 100 GLU cc_start: 0.8286 (tp30) cc_final: 0.8051 (tp30) REVERT: H 71 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7144 (tt) REVERT: H 99 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7700 (t) REVERT: I 71 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7105 (tt) REVERT: J 71 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7085 (tt) REVERT: J 99 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7649 (t) outliers start: 68 outliers final: 57 residues processed: 232 average time/residue: 0.2296 time to fit residues: 88.7601 Evaluate side-chains 256 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.139682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107753 restraints weight = 36137.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.110820 restraints weight = 18971.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.112820 restraints weight = 12495.386| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16893 Z= 0.236 Angle : 0.719 10.742 23028 Z= 0.371 Chirality : 0.045 0.152 2517 Planarity : 0.004 0.051 2973 Dihedral : 5.471 21.351 2313 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.23 % Allowed : 24.47 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.18), residues: 2118 helix: 1.45 (0.28), residues: 324 sheet: -1.44 (0.23), residues: 561 loop : -2.44 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 118 HIS 0.009 0.001 HIS N 66 PHE 0.016 0.002 PHE A 436 TYR 0.032 0.002 TYR J 55 ARG 0.002 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 540) hydrogen bonds : angle 5.66566 ( 1521) SS BOND : bond 0.00509 ( 24) SS BOND : angle 1.64119 ( 48) covalent geometry : bond 0.00541 (16869) covalent geometry : angle 0.71535 (22980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 187 time to evaluate : 1.812 Fit side-chains REVERT: A 100 GLU cc_start: 0.8369 (tp30) cc_final: 0.8151 (tp30) REVERT: A 343 MET cc_start: 0.6655 (mmm) cc_final: 0.6434 (mmm) REVERT: A 403 MET cc_start: 0.7955 (tpp) cc_final: 0.7740 (tpp) REVERT: B 403 MET cc_start: 0.8048 (tpp) cc_final: 0.7732 (tpp) REVERT: C 100 GLU cc_start: 0.8356 (tp30) cc_final: 0.8126 (tp30) REVERT: H 71 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7057 (tt) REVERT: H 99 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7697 (t) REVERT: I 71 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6966 (tt) REVERT: J 71 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6930 (tt) REVERT: J 99 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7636 (t) outliers start: 74 outliers final: 64 residues processed: 228 average time/residue: 0.2299 time to fit residues: 88.4761 Evaluate side-chains 253 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 184 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 201 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 125 optimal weight: 0.0050 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.141874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110004 restraints weight = 36045.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.113165 restraints weight = 18805.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.115177 restraints weight = 12324.141| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16893 Z= 0.149 Angle : 0.676 10.251 23028 Z= 0.349 Chirality : 0.044 0.159 2517 Planarity : 0.004 0.046 2973 Dihedral : 5.283 20.245 2313 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.66 % Allowed : 24.99 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.18), residues: 2118 helix: 1.57 (0.29), residues: 324 sheet: -1.39 (0.23), residues: 567 loop : -2.32 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 110 HIS 0.009 0.001 HIS N 66 PHE 0.009 0.001 PHE L 87 TYR 0.029 0.001 TYR I 55 ARG 0.003 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 540) hydrogen bonds : angle 5.54579 ( 1521) SS BOND : bond 0.00447 ( 24) SS BOND : angle 1.51193 ( 48) covalent geometry : bond 0.00344 (16869) covalent geometry : angle 0.67287 (22980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 1.721 Fit side-chains REVERT: A 100 GLU cc_start: 0.8333 (tp30) cc_final: 0.8103 (tp30) REVERT: A 343 MET cc_start: 0.6593 (mmm) cc_final: 0.5802 (tmm) REVERT: B 403 MET cc_start: 0.8024 (tpp) cc_final: 0.7729 (tpp) REVERT: C 100 GLU cc_start: 0.8314 (tp30) cc_final: 0.8084 (tp30) REVERT: H 71 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7073 (tt) REVERT: H 99 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7669 (t) REVERT: I 71 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7027 (tt) REVERT: J 71 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7067 (tt) REVERT: J 99 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7634 (t) REVERT: N 55 TYR cc_start: 0.7470 (p90) cc_final: 0.7078 (p90) outliers start: 64 outliers final: 56 residues processed: 233 average time/residue: 0.2144 time to fit residues: 83.4943 Evaluate side-chains 253 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain M residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.143237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111401 restraints weight = 35885.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.114577 restraints weight = 18638.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.116560 restraints weight = 12190.074| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16893 Z= 0.133 Angle : 0.671 10.061 23028 Z= 0.344 Chirality : 0.044 0.152 2517 Planarity : 0.004 0.045 2973 Dihedral : 5.150 20.317 2313 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.32 % Allowed : 25.39 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.18), residues: 2118 helix: 1.60 (0.29), residues: 324 sheet: -1.29 (0.23), residues: 570 loop : -2.25 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 110 HIS 0.008 0.001 HIS N 66 PHE 0.019 0.001 PHE A 436 TYR 0.048 0.002 TYR L 55 ARG 0.004 0.000 ARG I 120 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 540) hydrogen bonds : angle 5.46322 ( 1521) SS BOND : bond 0.00391 ( 24) SS BOND : angle 1.43924 ( 48) covalent geometry : bond 0.00307 (16869) covalent geometry : angle 0.66829 (22980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 1.828 Fit side-chains REVERT: A 100 GLU cc_start: 0.8324 (tp30) cc_final: 0.8080 (tp30) REVERT: A 343 MET cc_start: 0.6585 (mmm) cc_final: 0.6278 (mmm) REVERT: C 100 GLU cc_start: 0.8318 (tp30) cc_final: 0.8078 (tp30) REVERT: C 403 MET cc_start: 0.7956 (tpp) cc_final: 0.7498 (tpp) REVERT: H 71 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7092 (tt) REVERT: H 99 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7649 (t) REVERT: I 71 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7041 (tt) REVERT: J 71 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7058 (tt) REVERT: J 99 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7596 (t) outliers start: 58 outliers final: 52 residues processed: 237 average time/residue: 0.2181 time to fit residues: 85.9898 Evaluate side-chains 253 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 176 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.138174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106219 restraints weight = 36474.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.109243 restraints weight = 19175.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.111211 restraints weight = 12664.525| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 16893 Z= 0.303 Angle : 0.776 10.118 23028 Z= 0.401 Chirality : 0.047 0.180 2517 Planarity : 0.005 0.048 2973 Dihedral : 5.589 23.357 2313 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 3.83 % Allowed : 25.10 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.18), residues: 2118 helix: 1.12 (0.28), residues: 324 sheet: -1.44 (0.23), residues: 564 loop : -2.41 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP H 118 HIS 0.012 0.002 HIS N 66 PHE 0.017 0.002 PHE H 87 TYR 0.035 0.002 TYR H 55 ARG 0.003 0.000 ARG I 120 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 540) hydrogen bonds : angle 5.73556 ( 1521) SS BOND : bond 0.00610 ( 24) SS BOND : angle 1.84753 ( 48) covalent geometry : bond 0.00696 (16869) covalent geometry : angle 0.77249 (22980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8231.51 seconds wall clock time: 147 minutes 10.35 seconds (8830.35 seconds total)