Starting phenix.real_space_refine on Sun May 18 02:41:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v7o_43008/05_2025/8v7o_43008_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v7o_43008/05_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_43008/05_2025/8v7o_43008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v7o_43008/05_2025/8v7o_43008.map" model { file = "/net/cci-nas-00/data/ceres_data/8v7o_43008/05_2025/8v7o_43008_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v7o_43008/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.90, per 1000 atoms: 0.66 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: 4.04 Conformation dependent library (CDL) restraints added in 2.0 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: 2.44 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: 4.70 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: 0.12 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: 15.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.940 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 39.250 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.120 ------------------------------------------------------------------------------- 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 : 1.822 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: 0.2455 time to fit residues: 89.4285 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 : 1.971 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.117844 restraints weight = 35684.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.120950 restraints weight = 18978.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.122996 restraints weight = 12530.950| |-----------------------------------------------------------------------------| 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 : 1.772 Fit side-chains REVERT: A 103 GLU cc_start: 0.8471 (tp30) cc_final: 0.8231 (tt0) REVERT: A 403 MET cc_start: 0.8014 (tpp) cc_final: 0.7706 (tpp) REVERT: B 103 GLU cc_start: 0.8467 (tp30) cc_final: 0.8201 (tt0) REVERT: B 343 MET cc_start: 0.6527 (mmm) cc_final: 0.6314 (mmm) REVERT: B 403 MET cc_start: 0.8033 (tpp) cc_final: 0.7786 (tpp) REVERT: C 103 GLU cc_start: 0.8487 (tp30) cc_final: 0.8160 (tt0) REVERT: C 403 MET cc_start: 0.7972 (tpp) cc_final: 0.7716 (tpp) outliers start: 36 outliers final: 30 residues processed: 253 average time/residue: 0.2455 time to fit residues: 99.5161 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 : 1.987 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.0570 chunk 66 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- 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 ** 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 405 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.145142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.113220 restraints weight = 35344.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.116179 restraints weight = 19268.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.118138 restraints weight = 12983.985| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16893 Z= 0.247 Angle : 0.784 10.451 23028 Z= 0.402 Chirality : 0.047 0.155 2517 Planarity : 0.005 0.060 2973 Dihedral : 5.967 22.090 2313 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 3.14 % Allowed : 17.90 % Favored : 78.96 % 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: -2.51 (0.18), residues: 2118 helix: 1.07 (0.28), residues: 342 sheet: -1.72 (0.22), residues: 585 loop : -2.57 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 111A HIS 0.008 0.001 HIS B 180 PHE 0.016 0.002 PHE H 87 TYR 0.034 0.002 TYR H 55 ARG 0.004 0.001 ARG C 216 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 540) hydrogen bonds : angle 6.16158 ( 1521) SS BOND : bond 0.00601 ( 24) SS BOND : angle 1.85910 ( 48) covalent geometry : bond 0.00563 (16869) covalent geometry : angle 0.78014 (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 257 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 1.846 Fit side-chains REVERT: A 100 GLU cc_start: 0.8248 (tp30) cc_final: 0.8044 (tp30) REVERT: A 403 MET cc_start: 0.8052 (tpp) cc_final: 0.7763 (tpp) outliers start: 55 outliers final: 48 residues processed: 228 average time/residue: 0.2250 time to fit residues: 85.2694 Evaluate side-chains 240 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 110 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 176 optimal weight: 0.4980 chunk 209 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.147361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.115916 restraints weight = 35645.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.119028 restraints weight = 18896.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.121071 restraints weight = 12499.030| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16893 Z= 0.150 Angle : 0.698 8.245 23028 Z= 0.359 Chirality : 0.045 0.157 2517 Planarity : 0.004 0.057 2973 Dihedral : 5.611 20.829 2313 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.43 % Allowed : 20.81 % Favored : 75.76 % 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: -2.32 (0.18), residues: 2118 helix: 1.29 (0.29), residues: 342 sheet: -1.60 (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 L 41 HIS 0.005 0.001 HIS B 180 PHE 0.012 0.001 PHE C 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 0.04036 ( 540) hydrogen bonds : angle 5.84179 ( 1521) SS BOND : bond 0.00430 ( 24) SS BOND : angle 1.63103 ( 48) covalent geometry : bond 0.00344 (16869) covalent geometry : angle 0.69493 (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 276 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 1.853 Fit side-chains REVERT: A 100 GLU cc_start: 0.8238 (tp30) cc_final: 0.7983 (tp30) REVERT: A 343 MET cc_start: 0.6404 (mmm) cc_final: 0.6038 (tmm) REVERT: A 403 MET cc_start: 0.8029 (tpp) cc_final: 0.7752 (tpp) REVERT: B 343 MET cc_start: 0.6428 (mmm) cc_final: 0.6001 (tmm) REVERT: C 100 GLU cc_start: 0.8265 (tp30) cc_final: 0.8047 (tp30) REVERT: H 99 THR cc_start: 0.8049 (t) cc_final: 0.7807 (t) REVERT: I 99 THR cc_start: 0.7907 (t) cc_final: 0.7697 (t) REVERT: J 99 THR cc_start: 0.7916 (t) cc_final: 0.7674 (t) REVERT: J 111 TRP cc_start: 0.7815 (m-10) cc_final: 0.7601 (m-10) outliers start: 60 outliers final: 47 residues processed: 245 average time/residue: 0.2316 time to fit residues: 92.1382 Evaluate side-chains 244 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 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 426 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 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: 9.9990 chunk 14 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.144573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.113127 restraints weight = 36653.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116207 restraints weight = 19171.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.118221 restraints weight = 12581.226| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2013 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= 0.191 Angle : 0.702 7.444 23028 Z= 0.362 Chirality : 0.045 0.162 2517 Planarity : 0.004 0.054 2973 Dihedral : 5.528 20.519 2313 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.83 % Allowed : 22.98 % Favored : 73.18 % 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: -2.25 (0.18), residues: 2118 helix: 1.65 (0.29), residues: 321 sheet: -1.56 (0.22), residues: 582 loop : -2.45 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 118 HIS 0.006 0.001 HIS B 180 PHE 0.012 0.002 PHE H 87 TYR 0.031 0.002 TYR H 55 ARG 0.011 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 540) hydrogen bonds : angle 5.73078 ( 1521) SS BOND : bond 0.00457 ( 24) SS BOND : angle 1.60697 ( 48) covalent geometry : bond 0.00439 (16869) covalent geometry : angle 0.69894 (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 274 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 207 time to evaluate : 1.995 Fit side-chains REVERT: A 100 GLU cc_start: 0.8266 (tp30) cc_final: 0.8034 (tp30) REVERT: A 343 MET cc_start: 0.6529 (mmm) cc_final: 0.5963 (tmm) REVERT: A 403 MET cc_start: 0.8063 (tpp) cc_final: 0.7831 (tpp) REVERT: B 403 MET cc_start: 0.8093 (tpp) cc_final: 0.7867 (tpp) REVERT: C 100 GLU cc_start: 0.8280 (tp30) cc_final: 0.8056 (tp30) REVERT: C 403 MET cc_start: 0.8007 (tpp) cc_final: 0.7721 (tpp) REVERT: H 99 THR cc_start: 0.8035 (t) cc_final: 0.7809 (t) REVERT: I 99 THR cc_start: 0.7884 (t) cc_final: 0.7676 (t) REVERT: J 99 THR cc_start: 0.7904 (t) cc_final: 0.7668 (t) outliers start: 67 outliers final: 59 residues processed: 242 average time/residue: 0.2331 time to fit residues: 93.7503 Evaluate side-chains 252 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 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 89 THR 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 43 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ** 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.140535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108549 restraints weight = 36121.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.111627 restraints weight = 19043.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.113641 restraints weight = 12580.098| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16893 Z= 0.209 Angle : 0.703 7.576 23028 Z= 0.364 Chirality : 0.045 0.156 2517 Planarity : 0.004 0.053 2973 Dihedral : 5.527 20.820 2313 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.89 % Allowed : 24.41 % Favored : 71.70 % 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: -2.25 (0.18), residues: 2118 helix: 1.54 (0.29), residues: 324 sheet: -1.54 (0.22), residues: 576 loop : -2.43 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 118 HIS 0.006 0.001 HIS L 66 PHE 0.013 0.002 PHE B 436 TYR 0.032 0.002 TYR I 55 ARG 0.004 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 540) hydrogen bonds : angle 5.72105 ( 1521) SS BOND : bond 0.00474 ( 24) SS BOND : angle 1.62325 ( 48) covalent geometry : bond 0.00482 (16869) covalent geometry : angle 0.69984 (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 262 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 1.794 Fit side-chains REVERT: A 100 GLU cc_start: 0.8355 (tp30) cc_final: 0.8126 (tp30) REVERT: A 343 MET cc_start: 0.6628 (mmm) cc_final: 0.5823 (tmm) REVERT: A 403 MET cc_start: 0.8054 (tpp) cc_final: 0.7760 (tpp) REVERT: C 100 GLU cc_start: 0.8344 (tp30) cc_final: 0.8111 (tp30) REVERT: H 99 THR cc_start: 0.7969 (t) cc_final: 0.7746 (t) REVERT: J 99 THR cc_start: 0.7855 (t) cc_final: 0.7632 (t) outliers start: 68 outliers final: 59 residues processed: 228 average time/residue: 0.2324 time to fit residues: 87.2829 Evaluate side-chains 247 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 188 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 70 LEU 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 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 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 M 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: 0.9990 chunk 25 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ** 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.143169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.111362 restraints weight = 35898.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.114529 restraints weight = 18770.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.116590 restraints weight = 12323.393| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2268 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= 0.143 Angle : 0.674 11.261 23028 Z= 0.346 Chirality : 0.044 0.162 2517 Planarity : 0.004 0.051 2973 Dihedral : 5.278 20.409 2313 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.66 % Allowed : 24.76 % Favored : 71.58 % 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: -2.10 (0.18), residues: 2118 helix: 1.71 (0.29), residues: 324 sheet: -1.48 (0.22), residues: 576 loop : -2.33 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 118 HIS 0.005 0.001 HIS N 66 PHE 0.008 0.001 PHE H 112A TYR 0.028 0.001 TYR I 55 ARG 0.004 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 540) hydrogen bonds : angle 5.56709 ( 1521) SS BOND : bond 0.00404 ( 24) SS BOND : angle 1.47341 ( 48) covalent geometry : bond 0.00331 (16869) covalent geometry : angle 0.67099 (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 276 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 1.910 Fit side-chains REVERT: A 100 GLU cc_start: 0.8324 (tp30) cc_final: 0.8075 (tp30) REVERT: A 343 MET cc_start: 0.6595 (mmm) cc_final: 0.6274 (mmm) REVERT: A 403 MET cc_start: 0.8040 (tpp) cc_final: 0.7792 (tpp) REVERT: C 100 GLU cc_start: 0.8314 (tp30) cc_final: 0.8071 (tp30) REVERT: H 71 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7095 (tt) REVERT: H 99 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7667 (t) REVERT: I 71 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7047 (tt) REVERT: J 71 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7034 (tt) REVERT: J 99 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7627 (t) outliers start: 64 outliers final: 51 residues processed: 243 average time/residue: 0.2189 time to fit residues: 87.9560 Evaluate side-chains 248 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.9990 chunk 14 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 158 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 ** 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 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 = 0.4078 r_free = 0.4078 target = 0.140213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.108288 restraints weight = 36067.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111385 restraints weight = 18895.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.113348 restraints weight = 12421.595| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16893 Z= 0.212 Angle : 0.709 10.680 23028 Z= 0.364 Chirality : 0.045 0.168 2517 Planarity : 0.004 0.048 2973 Dihedral : 5.393 20.936 2313 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.35 % Allowed : 24.47 % Favored : 71.18 % 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: -2.17 (0.18), residues: 2118 helix: 1.51 (0.28), residues: 324 sheet: -1.40 (0.23), residues: 564 loop : -2.39 (0.16), residues: 1230 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 0.031 0.002 TYR J 55 ARG 0.004 0.000 ARG I 120 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 540) hydrogen bonds : angle 5.61039 ( 1521) SS BOND : bond 0.00479 ( 24) SS BOND : angle 1.59488 ( 48) covalent geometry : bond 0.00490 (16869) covalent geometry : angle 0.70597 (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 269 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 193 time to evaluate : 1.824 Fit side-chains REVERT: A 100 GLU cc_start: 0.8356 (tp30) cc_final: 0.8139 (tp30) REVERT: A 343 MET cc_start: 0.6662 (mmm) cc_final: 0.6338 (mmm) REVERT: A 403 MET cc_start: 0.8066 (tpp) cc_final: 0.7807 (tpp) REVERT: B 403 MET cc_start: 0.8118 (tpp) cc_final: 0.7917 (tpp) REVERT: C 100 GLU cc_start: 0.8350 (tp30) cc_final: 0.8119 (tp30) REVERT: C 403 MET cc_start: 0.8054 (tpp) cc_final: 0.7837 (tpp) REVERT: H 71 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7052 (tt) REVERT: H 99 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7650 (t) REVERT: I 71 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6991 (tt) REVERT: J 71 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6981 (tt) REVERT: J 99 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7626 (t) outliers start: 76 outliers final: 64 residues processed: 234 average time/residue: 0.2282 time to fit residues: 88.6510 Evaluate side-chains 258 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 399 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 419 THR 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 419 THR 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 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 30 ILE 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 25 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 201 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 190 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 204 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 HIS ** 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** ** C 8 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** L 48 GLN M 48 GLN M 66 HIS N 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.148036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.117295 restraints weight = 34424.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.120490 restraints weight = 18185.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.122530 restraints weight = 11928.937| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16893 Z= 0.122 Angle : 0.660 10.315 23028 Z= 0.338 Chirality : 0.044 0.154 2517 Planarity : 0.004 0.044 2973 Dihedral : 5.082 20.463 2313 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.26 % Allowed : 25.61 % Favored : 71.13 % 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: -1.97 (0.18), residues: 2118 helix: 1.76 (0.29), residues: 324 sheet: -1.36 (0.23), residues: 582 loop : -2.24 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 111A HIS 0.006 0.001 HIS N 66 PHE 0.007 0.001 PHE H 112A TYR 0.027 0.001 TYR I 55 ARG 0.005 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 540) hydrogen bonds : angle 5.41944 ( 1521) SS BOND : bond 0.00347 ( 24) SS BOND : angle 1.38641 ( 48) covalent geometry : bond 0.00280 (16869) covalent geometry : angle 0.65741 (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 271 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 2.042 Fit side-chains REVERT: A 100 GLU cc_start: 0.8337 (tp30) cc_final: 0.8086 (tp30) REVERT: A 343 MET cc_start: 0.6647 (mmm) cc_final: 0.6342 (mmm) REVERT: A 403 MET cc_start: 0.8009 (tpp) cc_final: 0.7770 (tpp) REVERT: B 403 MET cc_start: 0.8082 (tpp) cc_final: 0.7871 (tpp) REVERT: C 100 GLU cc_start: 0.8335 (tp30) cc_final: 0.8099 (tp30) REVERT: C 403 MET cc_start: 0.8031 (tpp) cc_final: 0.7817 (tpp) REVERT: H 71 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7109 (tt) REVERT: H 99 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7651 (t) REVERT: I 71 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7111 (tt) REVERT: I 111 TRP cc_start: 0.7837 (m100) cc_final: 0.7505 (m100) REVERT: I 112 ASP cc_start: 0.7737 (t70) cc_final: 0.7504 (t0) REVERT: J 71 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7027 (tt) REVERT: J 99 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7599 (t) REVERT: L 55 TYR cc_start: 0.7338 (p90) cc_final: 0.7132 (p90) outliers start: 57 outliers final: 48 residues processed: 241 average time/residue: 0.2276 time to fit residues: 90.2223 Evaluate side-chains 253 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** ** 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 8 HIS ** 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** 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 = 0.4118 r_free = 0.4118 target = 0.143773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.111973 restraints weight = 35880.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.115133 restraints weight = 18834.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.117168 restraints weight = 12381.973| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2586 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= 0.156 Angle : 0.679 10.057 23028 Z= 0.348 Chirality : 0.044 0.153 2517 Planarity : 0.004 0.044 2973 Dihedral : 5.099 19.994 2313 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.20 % Allowed : 26.13 % Favored : 70.67 % 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: -1.92 (0.18), residues: 2118 helix: 1.68 (0.28), residues: 324 sheet: -1.25 (0.23), residues: 570 loop : -2.21 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 111A HIS 0.009 0.001 HIS L 66 PHE 0.019 0.001 PHE C 436 TYR 0.029 0.002 TYR H 55 ARG 0.005 0.000 ARG H 120 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 540) hydrogen bonds : angle 5.42928 ( 1521) SS BOND : bond 0.00423 ( 24) SS BOND : angle 1.93149 ( 48) covalent geometry : bond 0.00360 (16869) covalent geometry : angle 0.67443 (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 257 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 1.902 Fit side-chains REVERT: A 100 GLU cc_start: 0.8322 (tp30) cc_final: 0.8090 (tp30) REVERT: A 343 MET cc_start: 0.6646 (mmm) cc_final: 0.6303 (mmm) REVERT: A 403 MET cc_start: 0.8042 (tpp) cc_final: 0.7767 (tpp) REVERT: C 100 GLU cc_start: 0.8341 (tp30) cc_final: 0.8109 (tp30) REVERT: C 403 MET cc_start: 0.8030 (tpp) cc_final: 0.7765 (tpp) REVERT: H 71 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7046 (tt) REVERT: I 71 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7012 (tt) REVERT: I 84 LYS cc_start: 0.8485 (mttm) cc_final: 0.8154 (mmtt) REVERT: J 71 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6972 (tt) REVERT: J 99 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7593 (t) outliers start: 56 outliers final: 48 residues processed: 230 average time/residue: 0.2155 time to fit residues: 82.3502 Evaluate side-chains 249 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 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 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 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 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 416 ASP Chi-restraints excluded: chain C residue 426 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 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 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: 0.4980 chunk 176 optimal weight: 0.2980 chunk 138 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** ** 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 ** 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 8 HIS ** 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** 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 = 0.4115 r_free = 0.4115 target = 0.143077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111266 restraints weight = 36163.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.114441 restraints weight = 18803.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.116510 restraints weight = 12294.168| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16893 Z= 0.157 Angle : 0.682 9.974 23028 Z= 0.350 Chirality : 0.044 0.178 2517 Planarity : 0.004 0.045 2973 Dihedral : 5.110 19.844 2313 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.32 % Allowed : 26.07 % Favored : 70.61 % 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: -1.91 (0.18), residues: 2118 helix: 1.66 (0.28), residues: 324 sheet: -1.23 (0.23), residues: 570 loop : -2.20 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 111A HIS 0.008 0.001 HIS L 66 PHE 0.009 0.001 PHE H 87 TYR 0.030 0.002 TYR I 113 ARG 0.005 0.000 ARG M 67 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 540) hydrogen bonds : angle 5.43458 ( 1521) SS BOND : bond 0.00416 ( 24) SS BOND : angle 1.98402 ( 48) covalent geometry : bond 0.00364 (16869) covalent geometry : angle 0.67665 (22980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6804.42 seconds wall clock time: 120 minutes 59.06 seconds (7259.06 seconds total)