Starting phenix.real_space_refine on Sat Oct 11 17:35:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v7o_43008/10_2025/8v7o_43008_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v7o_43008/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v7o_43008/10_2025/8v7o_43008_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v7o_43008/10_2025/8v7o_43008_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v7o_43008/10_2025/8v7o_43008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v7o_43008/10_2025/8v7o_43008.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'PHE:plan': 1, '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: {'GLU:plan': 6, 'PHE:plan': 1, '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: {'GLU:plan': 6, 'PHE:plan': 1, '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: {'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE: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: {'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE: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: {'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE: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: {'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG: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: {'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG: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: {'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 3.86, per 1000 atoms: 0.23 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: 1.41 Conformation dependent library (CDL) restraints added in 737.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.70 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: 2.94 Time building geometry restraints manager: 1.85 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.930 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: 0.640 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.230 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- 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 : 24.94 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.97 (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 ARG 0.009 0.001 ARG B 216 TYR 0.035 0.003 TYR A 305 PHE 0.023 0.003 PHE N 87 TRP 0.075 0.005 TRP B 149 HIS 0.008 0.002 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00621 (16869) covalent geometry : angle 0.97236 (22980) SS BOND : bond 0.00631 ( 24) SS BOND : angle 2.46197 ( 48) hydrogen bonds : bond 0.24530 ( 540) hydrogen bonds : angle 9.44913 ( 1521) *********************** 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 : 0.678 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: 0.1174 time to fit residues: 43.4189 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 : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.0020 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- 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 ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4128 r_free = 0.4128 target = 0.143152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.111845 restraints weight = 36620.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.114859 restraints weight = 19286.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.116728 restraints weight = 12717.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.118079 restraints weight = 9709.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.118774 restraints weight = 8132.036| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16893 Z= 0.208 Angle : 0.833 13.183 23028 Z= 0.424 Chirality : 0.048 0.161 2517 Planarity : 0.005 0.060 2973 Dihedral : 6.259 22.695 2313 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.29 % Allowed : 12.98 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.18), residues: 2118 helix: 0.73 (0.28), residues: 342 sheet: -1.71 (0.22), residues: 579 loop : -2.63 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 216 TYR 0.036 0.002 TYR J 55 PHE 0.021 0.002 PHE I 112A TRP 0.028 0.003 TRP C 149 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00475 (16869) covalent geometry : angle 0.82821 (22980) SS BOND : bond 0.00571 ( 24) SS BOND : angle 2.06360 ( 48) hydrogen bonds : bond 0.05077 ( 540) hydrogen bonds : angle 6.71541 ( 1521) *********************** 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 250 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.672 Fit side-chains REVERT: A 103 GLU cc_start: 0.8529 (tp30) cc_final: 0.8241 (tt0) REVERT: A 343 MET cc_start: 0.6314 (mmm) cc_final: 0.5740 (tmm) REVERT: A 403 MET cc_start: 0.8027 (tpp) cc_final: 0.7756 (tpp) REVERT: B 103 GLU cc_start: 0.8526 (tp30) cc_final: 0.8201 (tt0) REVERT: B 343 MET cc_start: 0.6555 (mmm) cc_final: 0.6333 (mmm) REVERT: B 403 MET cc_start: 0.8078 (tpp) cc_final: 0.7841 (tpp) REVERT: C 103 GLU cc_start: 0.8536 (tp30) cc_final: 0.8184 (tt0) REVERT: C 403 MET cc_start: 0.8003 (tpp) cc_final: 0.7777 (tpp) outliers start: 40 outliers final: 36 residues processed: 224 average time/residue: 0.1137 time to fit residues: 41.3208 Evaluate side-chains 228 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 381 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 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 381 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 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 426 VAL Chi-restraints excluded: chain C residue 441 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 12 LEU Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 42 ILE 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 93 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 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 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 = 0.4103 r_free = 0.4103 target = 0.141452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109731 restraints weight = 37032.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.112749 restraints weight = 19589.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.114668 restraints weight = 12965.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.115918 restraints weight = 9893.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.116664 restraints weight = 8324.076| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1520 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= 0.260 Angle : 0.794 10.979 23028 Z= 0.408 Chirality : 0.047 0.158 2517 Planarity : 0.005 0.063 2973 Dihedral : 6.141 22.214 2313 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.32 % Allowed : 20.30 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.18), residues: 2118 helix: 0.85 (0.28), residues: 342 sheet: -1.78 (0.22), residues: 585 loop : -2.64 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 401 TYR 0.033 0.002 TYR H 55 PHE 0.016 0.002 PHE H 87 TRP 0.023 0.003 TRP H 118 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00599 (16869) covalent geometry : angle 0.78982 (22980) SS BOND : bond 0.00527 ( 24) SS BOND : angle 1.91320 ( 48) hydrogen bonds : bond 0.04745 ( 540) hydrogen bonds : angle 6.23259 ( 1521) *********************** 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 259 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 0.732 Fit side-chains REVERT: A 343 MET cc_start: 0.6534 (mmm) cc_final: 0.6029 (mmm) REVERT: A 403 MET cc_start: 0.8034 (tpp) cc_final: 0.7769 (tpp) REVERT: B 100 GLU cc_start: 0.8239 (tp30) cc_final: 0.8038 (tp30) REVERT: J 112 ASP cc_start: 0.7868 (t70) cc_final: 0.7608 (t0) REVERT: L 55 TYR cc_start: 0.7549 (p90) cc_final: 0.7343 (p90) outliers start: 58 outliers final: 52 residues processed: 226 average time/residue: 0.1043 time to fit residues: 39.7597 Evaluate side-chains 241 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 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 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 186 ASP 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 H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 ILE 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 42 ILE 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 42 ILE 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 92 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 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 = 0.4182 r_free = 0.4182 target = 0.151052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.119550 restraints weight = 35028.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.122704 restraints weight = 18609.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.124778 restraints weight = 12347.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.125891 restraints weight = 9375.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.126779 restraints weight = 7937.582| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1940 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= 0.126 Angle : 0.686 8.273 23028 Z= 0.354 Chirality : 0.044 0.158 2517 Planarity : 0.004 0.059 2973 Dihedral : 5.570 21.006 2313 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.49 % Allowed : 22.18 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.18), residues: 2118 helix: 1.56 (0.29), residues: 318 sheet: -1.52 (0.23), residues: 552 loop : -2.43 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 216 TYR 0.027 0.001 TYR H 55 PHE 0.012 0.001 PHE B 436 TRP 0.016 0.002 TRP H 118 HIS 0.003 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00284 (16869) covalent geometry : angle 0.68280 (22980) SS BOND : bond 0.00398 ( 24) SS BOND : angle 1.54601 ( 48) hydrogen bonds : bond 0.04070 ( 540) hydrogen bonds : angle 5.78407 ( 1521) *********************** 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 298 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 0.700 Fit side-chains REVERT: A 343 MET cc_start: 0.6464 (mmm) cc_final: 0.6252 (mmm) REVERT: A 403 MET cc_start: 0.7990 (tpp) cc_final: 0.7719 (tpp) REVERT: B 343 MET cc_start: 0.6361 (mmm) cc_final: 0.5945 (tmm) REVERT: H 99 THR cc_start: 0.8101 (t) cc_final: 0.7864 (t) REVERT: I 99 THR cc_start: 0.7990 (t) cc_final: 0.7786 (t) REVERT: J 99 THR cc_start: 0.7961 (t) cc_final: 0.7721 (t) REVERT: J 112 ASP cc_start: 0.7652 (t70) cc_final: 0.7386 (t0) outliers start: 61 outliers final: 43 residues processed: 267 average time/residue: 0.1029 time to fit residues: 45.9431 Evaluate side-chains 247 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 294 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 B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL 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 399 LEU Chi-restraints excluded: chain B residue 416 ASP 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 186 ASP 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 H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain N residue 5 THR 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 131 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 179 HIS ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 244 ASN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** 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 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.138339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106428 restraints weight = 36250.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109436 restraints weight = 19149.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111418 restraints weight = 12704.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.112692 restraints weight = 9688.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113404 restraints weight = 8111.406| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 16893 Z= 0.333 Angle : 0.807 9.002 23028 Z= 0.419 Chirality : 0.048 0.167 2517 Planarity : 0.005 0.058 2973 Dihedral : 6.015 24.417 2313 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 4.46 % Allowed : 24.70 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.18), residues: 2118 helix: 1.07 (0.28), residues: 324 sheet: -1.66 (0.23), residues: 561 loop : -2.59 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 67 TYR 0.035 0.003 TYR I 55 PHE 0.020 0.003 PHE H 87 TRP 0.025 0.003 TRP H 118 HIS 0.010 0.001 HIS M 66 Details of bonding type rmsd covalent geometry : bond 0.00759 (16869) covalent geometry : angle 0.80388 (22980) SS BOND : bond 0.00616 ( 24) SS BOND : angle 1.84685 ( 48) hydrogen bonds : bond 0.04523 ( 540) hydrogen bonds : angle 6.01427 ( 1521) *********************** 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 269 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 191 time to evaluate : 0.621 Fit side-chains REVERT: A 403 MET cc_start: 0.8056 (tpp) cc_final: 0.7795 (tpp) REVERT: B 403 MET cc_start: 0.8108 (tpp) cc_final: 0.7853 (tpp) REVERT: C 403 MET cc_start: 0.8029 (tpp) cc_final: 0.7791 (tpp) REVERT: H 99 THR cc_start: 0.8025 (t) cc_final: 0.7793 (t) REVERT: I 99 THR cc_start: 0.7943 (t) cc_final: 0.7724 (t) REVERT: I 112 ASP cc_start: 0.8130 (t70) cc_final: 0.7925 (t0) REVERT: J 99 THR cc_start: 0.7907 (t) cc_final: 0.7667 (t) REVERT: J 112 ASP cc_start: 0.8049 (t70) cc_final: 0.7827 (t0) outliers start: 78 outliers final: 65 residues processed: 232 average time/residue: 0.1020 time to fit residues: 39.6344 Evaluate side-chains 248 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 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 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 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 B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 419 THR 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 30 ILE Chi-restraints excluded: chain H residue 42 ILE 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 25 VAL Chi-restraints excluded: chain I residue 42 ILE 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 76 VAL Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 110 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 244 ASN ** 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 227 ASN C 244 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.142581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.110935 restraints weight = 35872.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114054 restraints weight = 18920.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.116057 restraints weight = 12484.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.117277 restraints weight = 9505.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.118136 restraints weight = 7995.425| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16893 Z= 0.160 Angle : 0.691 7.417 23028 Z= 0.360 Chirality : 0.045 0.159 2517 Planarity : 0.004 0.055 2973 Dihedral : 5.568 20.747 2313 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.66 % Allowed : 25.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.18), residues: 2118 helix: 1.50 (0.28), residues: 318 sheet: -1.60 (0.22), residues: 576 loop : -2.47 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 67 TYR 0.028 0.002 TYR I 55 PHE 0.014 0.001 PHE A 436 TRP 0.020 0.002 TRP H 118 HIS 0.008 0.001 HIS N 66 Details of bonding type rmsd covalent geometry : bond 0.00363 (16869) covalent geometry : angle 0.68819 (22980) SS BOND : bond 0.00459 ( 24) SS BOND : angle 1.55852 ( 48) hydrogen bonds : bond 0.03938 ( 540) hydrogen bonds : angle 5.69676 ( 1521) *********************** 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 272 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 208 time to evaluate : 0.623 Fit side-chains REVERT: A 403 MET cc_start: 0.8004 (tpp) cc_final: 0.7749 (tpp) REVERT: B 403 MET cc_start: 0.8062 (tpp) cc_final: 0.7822 (tpp) REVERT: C 343 MET cc_start: 0.6616 (mmm) cc_final: 0.6330 (mmm) REVERT: H 99 THR cc_start: 0.8019 (t) cc_final: 0.7802 (t) REVERT: I 99 THR cc_start: 0.7878 (t) cc_final: 0.7676 (t) REVERT: J 99 THR cc_start: 0.7932 (t) cc_final: 0.7711 (t) REVERT: J 112 ASP cc_start: 0.7802 (t70) cc_final: 0.7581 (t0) outliers start: 64 outliers final: 51 residues processed: 238 average time/residue: 0.1032 time to fit residues: 41.0076 Evaluate side-chains 247 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain A residue 204 HIS 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 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 399 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 186 ASP 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 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 12 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain M residue 39 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 123 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 179 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.141481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.109775 restraints weight = 36006.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.112859 restraints weight = 18811.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.114857 restraints weight = 12406.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.116196 restraints weight = 9402.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.117087 restraints weight = 7835.843| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16893 Z= 0.164 Angle : 0.688 8.849 23028 Z= 0.356 Chirality : 0.045 0.171 2517 Planarity : 0.004 0.051 2973 Dihedral : 5.412 20.604 2313 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.66 % Allowed : 25.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.18), residues: 2118 helix: 1.55 (0.29), residues: 321 sheet: -1.55 (0.22), residues: 576 loop : -2.43 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 67 TYR 0.027 0.002 TYR H 55 PHE 0.010 0.001 PHE H 87 TRP 0.019 0.002 TRP H 118 HIS 0.009 0.001 HIS N 66 Details of bonding type rmsd covalent geometry : bond 0.00381 (16869) covalent geometry : angle 0.68539 (22980) SS BOND : bond 0.00423 ( 24) SS BOND : angle 1.52902 ( 48) hydrogen bonds : bond 0.03861 ( 540) hydrogen bonds : angle 5.59763 ( 1521) *********************** 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 264 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 0.640 Fit side-chains REVERT: A 403 MET cc_start: 0.8006 (tpp) cc_final: 0.7764 (tpp) REVERT: B 403 MET cc_start: 0.8041 (tpp) cc_final: 0.7789 (tpp) REVERT: H 71 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7088 (tt) REVERT: H 99 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7755 (t) REVERT: I 71 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6972 (tt) REVERT: J 71 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7023 (tt) REVERT: J 99 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7702 (t) REVERT: J 112 ASP cc_start: 0.7791 (t70) cc_final: 0.7577 (t0) outliers start: 64 outliers final: 51 residues processed: 233 average time/residue: 0.0954 time to fit residues: 37.6589 Evaluate side-chains 251 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 195 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 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 392 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 186 ASP 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 474 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain M residue 39 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 119 optimal weight: 0.0050 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- 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 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 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 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.139700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.107840 restraints weight = 36313.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.110900 restraints weight = 19064.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.112920 restraints weight = 12592.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.114142 restraints weight = 9560.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114981 restraints weight = 8036.264| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16893 Z= 0.224 Angle : 0.720 11.233 23028 Z= 0.371 Chirality : 0.045 0.167 2517 Planarity : 0.004 0.052 2973 Dihedral : 5.496 21.375 2313 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.17 % Allowed : 26.13 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.18), residues: 2118 helix: 1.40 (0.28), residues: 324 sheet: -1.50 (0.23), residues: 558 loop : -2.45 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 67 TYR 0.032 0.002 TYR I 55 PHE 0.016 0.002 PHE B 436 TRP 0.021 0.002 TRP H 118 HIS 0.010 0.001 HIS M 66 Details of bonding type rmsd covalent geometry : bond 0.00515 (16869) covalent geometry : angle 0.71720 (22980) SS BOND : bond 0.00486 ( 24) SS BOND : angle 1.61370 ( 48) hydrogen bonds : bond 0.03912 ( 540) hydrogen bonds : angle 5.62645 ( 1521) *********************** 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 263 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 190 time to evaluate : 0.698 Fit side-chains REVERT: A 403 MET cc_start: 0.8029 (tpp) cc_final: 0.7801 (tpp) REVERT: B 403 MET cc_start: 0.8063 (tpp) cc_final: 0.7813 (tpp) REVERT: H 71 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7160 (tt) REVERT: H 99 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7767 (t) REVERT: I 71 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6992 (tt) REVERT: J 71 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7008 (tt) REVERT: J 99 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7735 (t) REVERT: N 55 TYR cc_start: 0.7705 (p90) cc_final: 0.7384 (p90) outliers start: 73 outliers final: 58 residues processed: 233 average time/residue: 0.1016 time to fit residues: 39.8730 Evaluate side-chains 251 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain A residue 204 HIS 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 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 392 VAL 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 B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L 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: 6.9990 chunk 77 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 ** 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 = 0.4086 r_free = 0.4086 target = 0.140920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109136 restraints weight = 36163.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.112224 restraints weight = 18922.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.114245 restraints weight = 12481.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115579 restraints weight = 9476.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.116379 restraints weight = 7899.885| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2348 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= 0.181 Angle : 0.701 11.224 23028 Z= 0.362 Chirality : 0.045 0.159 2517 Planarity : 0.004 0.051 2973 Dihedral : 5.405 20.271 2313 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 3.72 % Allowed : 26.59 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.18), residues: 2118 helix: 1.53 (0.28), residues: 321 sheet: -1.49 (0.23), residues: 570 loop : -2.40 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 67 TYR 0.029 0.002 TYR I 55 PHE 0.011 0.001 PHE H 87 TRP 0.019 0.002 TRP I 118 HIS 0.010 0.001 HIS M 66 Details of bonding type rmsd covalent geometry : bond 0.00418 (16869) covalent geometry : angle 0.69828 (22980) SS BOND : bond 0.00444 ( 24) SS BOND : angle 1.55926 ( 48) hydrogen bonds : bond 0.03826 ( 540) hydrogen bonds : angle 5.57241 ( 1521) *********************** 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 255 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 0.672 Fit side-chains REVERT: A 343 MET cc_start: 0.6500 (mmm) cc_final: 0.6025 (mmm) REVERT: A 403 MET cc_start: 0.8003 (tpp) cc_final: 0.7774 (tpp) REVERT: B 403 MET cc_start: 0.8059 (tpp) cc_final: 0.7808 (tpp) REVERT: H 71 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7092 (tt) REVERT: H 99 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7709 (t) REVERT: I 71 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6954 (tt) REVERT: J 71 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6972 (tt) REVERT: J 99 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7698 (t) REVERT: N 55 TYR cc_start: 0.7661 (p90) cc_final: 0.7396 (p90) outliers start: 65 outliers final: 56 residues processed: 226 average time/residue: 0.1057 time to fit residues: 40.7247 Evaluate side-chains 249 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 188 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain A residue 204 HIS 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 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 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 B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain 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 25 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 78 optimal weight: 0.0050 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 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** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 48 GLN N 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.142380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.110703 restraints weight = 36105.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.113834 restraints weight = 18763.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.115890 restraints weight = 12320.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.117183 restraints weight = 9332.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.117976 restraints weight = 7799.544| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2478 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= 0.139 Angle : 0.684 11.023 23028 Z= 0.352 Chirality : 0.045 0.184 2517 Planarity : 0.004 0.050 2973 Dihedral : 5.239 20.449 2313 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.37 % Allowed : 26.93 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.18), residues: 2118 helix: 1.62 (0.28), residues: 321 sheet: -1.39 (0.23), residues: 570 loop : -2.32 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 67 TYR 0.027 0.001 TYR I 55 PHE 0.018 0.001 PHE B 436 TRP 0.020 0.002 TRP L 110 HIS 0.008 0.001 HIS M 66 Details of bonding type rmsd covalent geometry : bond 0.00321 (16869) covalent geometry : angle 0.68150 (22980) SS BOND : bond 0.00403 ( 24) SS BOND : angle 1.46171 ( 48) hydrogen bonds : bond 0.03753 ( 540) hydrogen bonds : angle 5.51689 ( 1521) ********************** 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 266 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 0.710 Fit side-chains REVERT: A 343 MET cc_start: 0.6473 (mmm) cc_final: 0.5958 (mmm) REVERT: B 403 MET cc_start: 0.8045 (tpp) cc_final: 0.7747 (tpp) REVERT: H 71 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7060 (tt) REVERT: H 99 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7711 (t) REVERT: I 71 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6999 (tt) REVERT: J 71 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7050 (tt) REVERT: J 99 THR cc_start: 0.7898 (OUTLIER) cc_final: 0.7688 (t) REVERT: L 55 TYR cc_start: 0.7298 (p90) cc_final: 0.6905 (p90) REVERT: N 55 TYR cc_start: 0.7613 (p90) cc_final: 0.7311 (p90) outliers start: 59 outliers final: 52 residues processed: 239 average time/residue: 0.1061 time to fit residues: 41.7216 Evaluate side-chains 253 residues out of total 1860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 73 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 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 392 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain 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 25 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 118 TRP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 118 TRP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 118 TRP Chi-restraints excluded: chain M residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 17 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 173 optimal weight: 0.2980 chunk 152 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 overall best weight: 1.2580 ------------------------------------------------------------------------------- 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 437 HIS ** 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** ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.143263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111706 restraints weight = 35976.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.114838 restraints weight = 18775.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.116891 restraints weight = 12342.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.118211 restraints weight = 9348.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.118862 restraints weight = 7808.674| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2535 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 : 0.685 10.798 23028 Z= 0.352 Chirality : 0.044 0.178 2517 Planarity : 0.004 0.044 2973 Dihedral : 5.165 20.375 2313 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.37 % Allowed : 26.93 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.18), residues: 2118 helix: 1.54 (0.28), residues: 324 sheet: -1.33 (0.23), residues: 570 loop : -2.25 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 120 TYR 0.027 0.001 TYR I 55 PHE 0.008 0.001 PHE H 87 TRP 0.019 0.002 TRP L 110 HIS 0.009 0.001 HIS L 66 Details of bonding type rmsd covalent geometry : bond 0.00331 (16869) covalent geometry : angle 0.68060 (22980) SS BOND : bond 0.00415 ( 24) SS BOND : angle 1.78296 ( 48) hydrogen bonds : bond 0.03677 ( 540) hydrogen bonds : angle 5.47527 ( 1521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3964.09 seconds wall clock time: 69 minutes 11.28 seconds (4151.28 seconds total)