Starting phenix.real_space_refine on Sat Jun 28 09:35:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgf_38320/06_2025/8xgf_38320_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgf_38320/06_2025/8xgf_38320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xgf_38320/06_2025/8xgf_38320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgf_38320/06_2025/8xgf_38320.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgf_38320/06_2025/8xgf_38320_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgf_38320/06_2025/8xgf_38320_trim.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 264 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 156 5.16 5 C 11388 2.51 5 N 2472 2.21 5 O 2664 1.98 5 H 15612 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32292 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2596 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 153} Chain breaks: 1 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 95 Unusual residues: {'ACD': 1, 'MC3': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 49 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 10.48, per 1000 atoms: 0.32 Number of scatterers: 32292 At special positions: 0 Unit cell: (99.12, 96.88, 148.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 O 2664 8.00 N 2472 7.00 C 11388 6.00 H 15612 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.54 Conformation dependent library (CDL) restraints added in 2.4 seconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 74.4% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.824A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.504A pdb=" N ALA A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 222 Processing helix chain 'A' and resid 246 through 275 removed outlier: 3.674A pdb=" N LYS A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 46 removed outlier: 3.568A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR J 44 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 71 removed outlier: 3.503A pdb=" N ALA J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU J 91 " --> pdb=" O CYS J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 222 Processing helix chain 'J' and resid 246 through 275 removed outlier: 3.674A pdb=" N LYS J 250 " --> pdb=" O ARG J 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU J 275 " --> pdb=" O GLU J 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 46 removed outlier: 3.567A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.503A pdb=" N ALA B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 222 Processing helix chain 'B' and resid 246 through 275 removed outlier: 3.674A pdb=" N LYS B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 46 removed outlier: 3.567A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.503A pdb=" N ALA C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.840A pdb=" N LEU C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 222 Processing helix chain 'C' and resid 246 through 275 removed outlier: 3.674A pdb=" N LYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 46 removed outlier: 3.567A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.504A pdb=" N ALA D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 222 Processing helix chain 'D' and resid 246 through 275 removed outlier: 3.675A pdb=" N LYS D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 46 removed outlier: 3.568A pdb=" N VAL E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.503A pdb=" N ALA E 65 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 222 Processing helix chain 'E' and resid 246 through 275 removed outlier: 3.675A pdb=" N LYS E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 46 removed outlier: 3.567A pdb=" N VAL F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 removed outlier: 3.503A pdb=" N ALA F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU F 91 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 222 Processing helix chain 'F' and resid 246 through 275 removed outlier: 3.674A pdb=" N LYS F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 46 removed outlier: 3.567A pdb=" N VAL G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR G 44 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 removed outlier: 3.505A pdb=" N ALA G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 86 Processing helix chain 'G' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU G 91 " --> pdb=" O CYS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 222 Processing helix chain 'G' and resid 246 through 275 removed outlier: 3.674A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 46 removed outlier: 3.568A pdb=" N VAL H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR H 44 " --> pdb=" O ILE H 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 71 removed outlier: 3.503A pdb=" N ALA H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 86 Processing helix chain 'H' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU H 91 " --> pdb=" O CYS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 222 Processing helix chain 'H' and resid 246 through 275 removed outlier: 3.674A pdb=" N LYS H 250 " --> pdb=" O ARG H 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU H 275 " --> pdb=" O GLU H 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 46 removed outlier: 3.567A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR I 44 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 71 removed outlier: 3.503A pdb=" N ALA I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 87 through 100 removed outlier: 3.840A pdb=" N LEU I 91 " --> pdb=" O CYS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 222 Processing helix chain 'I' and resid 246 through 275 removed outlier: 3.674A pdb=" N LYS I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU I 275 " --> pdb=" O GLU I 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 46 removed outlier: 3.568A pdb=" N VAL K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 71 removed outlier: 3.504A pdb=" N ALA K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 86 Processing helix chain 'K' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU K 91 " --> pdb=" O CYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 222 Processing helix chain 'K' and resid 246 through 275 removed outlier: 3.675A pdb=" N LYS K 250 " --> pdb=" O ARG K 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU K 275 " --> pdb=" O GLU K 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 46 removed outlier: 3.567A pdb=" N VAL L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N THR L 44 " --> pdb=" O ILE L 40 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 71 removed outlier: 3.504A pdb=" N ALA L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 86 Processing helix chain 'L' and resid 87 through 100 removed outlier: 3.841A pdb=" N LEU L 91 " --> pdb=" O CYS L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 222 Processing helix chain 'L' and resid 246 through 275 removed outlier: 3.674A pdb=" N LYS L 250 " --> pdb=" O ARG L 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU L 275 " --> pdb=" O GLU L 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL J 54 " --> pdb=" O TYR J 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.652A pdb=" N VAL F 54 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.654A pdb=" N VAL G 54 " --> pdb=" O TYR G 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL H 54 " --> pdb=" O TYR H 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL I 54 " --> pdb=" O TYR I 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL K 54 " --> pdb=" O TYR K 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.652A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3240 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: 11.40 Time building geometry restraints manager: 10.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15576 1.03 - 1.23: 48 1.23 - 1.42: 6888 1.42 - 1.62: 9864 1.62 - 1.81: 204 Bond restraints: 32580 Sorted by residual: bond pdb=" C38 MC3 D 402 " pdb=" C39 MC3 D 402 " ideal model delta sigma weight residual 1.523 1.477 0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" C38 MC3 K 402 " pdb=" C39 MC3 K 402 " ideal model delta sigma weight residual 1.523 1.477 0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" C38 MC3 C 402 " pdb=" C39 MC3 C 402 " ideal model delta sigma weight residual 1.523 1.477 0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C38 MC3 J 402 " pdb=" C39 MC3 J 402 " ideal model delta sigma weight residual 1.523 1.477 0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" C38 MC3 I 402 " pdb=" C39 MC3 I 402 " ideal model delta sigma weight residual 1.523 1.477 0.046 2.00e-02 2.50e+03 5.18e+00 ... (remaining 32575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 57376 2.27 - 4.54: 272 4.54 - 6.81: 96 6.81 - 9.08: 36 9.08 - 11.35: 24 Bond angle restraints: 57804 Sorted by residual: angle pdb=" C38 MC3 L 401 " pdb=" C39 MC3 L 401 " pdb=" C40 MC3 L 401 " ideal model delta sigma weight residual 113.07 101.72 11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C38 MC3 E 401 " pdb=" C39 MC3 E 401 " pdb=" C40 MC3 E 401 " ideal model delta sigma weight residual 113.07 101.75 11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C38 MC3 J 401 " pdb=" C39 MC3 J 401 " pdb=" C40 MC3 J 401 " ideal model delta sigma weight residual 113.07 101.76 11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C38 MC3 B 401 " pdb=" C39 MC3 B 401 " pdb=" C40 MC3 B 401 " ideal model delta sigma weight residual 113.07 101.76 11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C38 MC3 H 401 " pdb=" C39 MC3 H 401 " pdb=" C40 MC3 H 401 " ideal model delta sigma weight residual 113.07 101.77 11.30 3.00e+00 1.11e-01 1.42e+01 ... (remaining 57799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 13776 16.38 - 32.76: 1428 32.76 - 49.14: 384 49.14 - 65.51: 216 65.51 - 81.89: 12 Dihedral angle restraints: 15816 sinusoidal: 8712 harmonic: 7104 Sorted by residual: dihedral pdb=" CA LYS E 238 " pdb=" CB LYS E 238 " pdb=" CG LYS E 238 " pdb=" CD LYS E 238 " ideal model delta sinusoidal sigma weight residual 60.00 117.83 -57.83 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA LYS H 238 " pdb=" CB LYS H 238 " pdb=" CG LYS H 238 " pdb=" CD LYS H 238 " ideal model delta sinusoidal sigma weight residual 60.00 117.82 -57.82 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA LYS F 238 " pdb=" CB LYS F 238 " pdb=" CG LYS F 238 " pdb=" CD LYS F 238 " ideal model delta sinusoidal sigma weight residual 60.00 117.82 -57.82 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 15813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1513 0.024 - 0.049: 494 0.049 - 0.073: 344 0.073 - 0.097: 126 0.097 - 0.122: 55 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CA VAL K 225 " pdb=" N VAL K 225 " pdb=" C VAL K 225 " pdb=" CB VAL K 225 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA VAL D 225 " pdb=" N VAL D 225 " pdb=" C VAL D 225 " pdb=" CB VAL D 225 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA ILE L 73 " pdb=" N ILE L 73 " pdb=" C ILE L 73 " pdb=" CB ILE L 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 2529 not shown) Planarity restraints: 4560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 246 " 0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO G 247 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO G 247 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 247 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 246 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 247 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 246 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO E 247 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 247 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 247 " -0.018 5.00e-02 4.00e+02 ... (remaining 4557 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 4960 2.30 - 2.87: 68781 2.87 - 3.45: 74024 3.45 - 4.02: 104274 4.02 - 4.60: 158483 Nonbonded interactions: 410522 Sorted by model distance: nonbonded pdb=" O SER K 245 " pdb=" HZ2 LYS K 250 " model vdw 1.722 2.450 nonbonded pdb=" O SER H 245 " pdb=" HZ2 LYS H 250 " model vdw 1.722 2.450 nonbonded pdb=" O SER L 245 " pdb=" HZ2 LYS L 250 " model vdw 1.722 2.450 nonbonded pdb=" O SER A 245 " pdb=" HZ2 LYS A 250 " model vdw 1.722 2.450 nonbonded pdb=" O SER D 245 " pdb=" HZ2 LYS D 250 " model vdw 1.722 2.450 ... (remaining 410517 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } 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 individual isotropic 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: 7.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.610 Extract box with map and model: 1.470 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 60.600 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.004 0.046 17004 Z= 0.207 Angle : 0.797 11.351 22692 Z= 0.333 Chirality : 0.039 0.122 2532 Planarity : 0.003 0.033 2736 Dihedral : 15.821 81.893 6408 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.20), residues: 1872 helix: 4.21 (0.13), residues: 1284 sheet: 1.55 (0.52), residues: 132 loop : -1.13 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP H 79 HIS 0.001 0.000 HIS J 99 PHE 0.008 0.001 PHE E 33 TYR 0.008 0.001 TYR G 218 ARG 0.002 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.09389 ( 1092) hydrogen bonds : angle 4.62583 ( 3240) SS BOND : bond 0.00130 ( 36) SS BOND : angle 0.63137 ( 72) covalent geometry : bond 0.00416 (16968) covalent geometry : angle 0.79734 (22620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.422 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 1.7561 time to fit residues: 564.3623 Evaluate side-chains 180 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 0.0670 chunk 77 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.188133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142817 restraints weight = 43058.897| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.54 r_work: 0.3657 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17004 Z= 0.108 Angle : 0.479 4.240 22692 Z= 0.250 Chirality : 0.039 0.129 2532 Planarity : 0.004 0.036 2736 Dihedral : 10.265 50.692 2904 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.40 % Allowed : 14.55 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.19), residues: 1872 helix: 3.82 (0.13), residues: 1284 sheet: 2.05 (0.57), residues: 132 loop : -1.45 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 79 HIS 0.002 0.001 HIS K 75 PHE 0.007 0.001 PHE C 33 TYR 0.007 0.001 TYR I 218 ARG 0.001 0.000 ARG I 233 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 1092) hydrogen bonds : angle 3.20270 ( 3240) SS BOND : bond 0.00168 ( 36) SS BOND : angle 0.86572 ( 72) covalent geometry : bond 0.00244 (16968) covalent geometry : angle 0.47681 (22620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 2.807 Fit side-chains REVERT: L 239 GLU cc_start: 0.8572 (tt0) cc_final: 0.8363 (tt0) outliers start: 42 outliers final: 24 residues processed: 247 average time/residue: 1.7121 time to fit residues: 495.3819 Evaluate side-chains 230 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 60 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.191457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145126 restraints weight = 43773.688| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.42 r_work: 0.3683 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 17004 Z= 0.090 Angle : 0.434 3.850 22692 Z= 0.227 Chirality : 0.038 0.122 2532 Planarity : 0.004 0.035 2736 Dihedral : 8.812 47.395 2904 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.28 % Allowed : 16.15 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.19), residues: 1872 helix: 3.88 (0.13), residues: 1284 sheet: 2.27 (0.58), residues: 132 loop : -1.33 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP J 79 HIS 0.001 0.000 HIS F 99 PHE 0.007 0.001 PHE G 33 TYR 0.006 0.001 TYR C 243 ARG 0.001 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 1092) hydrogen bonds : angle 3.01202 ( 3240) SS BOND : bond 0.00086 ( 36) SS BOND : angle 0.67756 ( 72) covalent geometry : bond 0.00195 (16968) covalent geometry : angle 0.43340 (22620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 2.506 Fit side-chains REVERT: J 220 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7800 (tt) REVERT: B 220 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7843 (tt) REVERT: C 220 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7820 (tt) REVERT: E 220 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7828 (tt) REVERT: F 220 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7812 (tt) REVERT: G 220 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7818 (tt) REVERT: I 220 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7838 (tt) REVERT: L 220 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7829 (tt) outliers start: 40 outliers final: 28 residues processed: 222 average time/residue: 1.8245 time to fit residues: 471.9677 Evaluate side-chains 227 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.192536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149524 restraints weight = 43217.880| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.33 r_work: 0.3611 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17004 Z= 0.149 Angle : 0.514 4.568 22692 Z= 0.270 Chirality : 0.041 0.132 2532 Planarity : 0.004 0.038 2736 Dihedral : 10.284 52.050 2904 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.40 % Allowed : 15.07 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.20), residues: 1872 helix: 3.60 (0.13), residues: 1284 sheet: 2.27 (0.59), residues: 132 loop : -1.34 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 79 HIS 0.004 0.001 HIS E 75 PHE 0.011 0.001 PHE G 33 TYR 0.008 0.002 TYR D 243 ARG 0.001 0.000 ARG J 246 Details of bonding type rmsd hydrogen bonds : bond 0.05489 ( 1092) hydrogen bonds : angle 3.13322 ( 3240) SS BOND : bond 0.00306 ( 36) SS BOND : angle 1.09978 ( 72) covalent geometry : bond 0.00369 (16968) covalent geometry : angle 0.51095 (22620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 2.355 Fit side-chains outliers start: 42 outliers final: 30 residues processed: 218 average time/residue: 1.8936 time to fit residues: 483.4072 Evaluate side-chains 211 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.185946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138712 restraints weight = 43372.100| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.42 r_work: 0.3516 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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 : 0.003 0.020 17004 Z= 0.112 Angle : 0.471 3.750 22692 Z= 0.247 Chirality : 0.039 0.130 2532 Planarity : 0.004 0.033 2736 Dihedral : 9.139 50.583 2904 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.11 % Allowed : 14.95 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.19), residues: 1872 helix: 3.61 (0.13), residues: 1284 sheet: 2.15 (0.57), residues: 132 loop : -1.33 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 79 HIS 0.002 0.001 HIS H 75 PHE 0.009 0.001 PHE C 33 TYR 0.007 0.001 TYR L 243 ARG 0.001 0.000 ARG L 233 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 1092) hydrogen bonds : angle 3.08759 ( 3240) SS BOND : bond 0.00163 ( 36) SS BOND : angle 0.91966 ( 72) covalent geometry : bond 0.00266 (16968) covalent geometry : angle 0.46900 (22620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 2.391 Fit side-chains REVERT: J 94 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 94 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7672 (tp) REVERT: C 94 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7781 (tp) REVERT: E 94 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7651 (tp) REVERT: F 94 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7793 (tp) REVERT: G 94 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7789 (tp) REVERT: I 94 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7680 (tp) REVERT: L 94 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7666 (tp) outliers start: 37 outliers final: 22 residues processed: 223 average time/residue: 1.8955 time to fit residues: 492.1428 Evaluate side-chains 214 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.184986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137940 restraints weight = 43834.738| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.42 r_work: 0.3503 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17004 Z= 0.121 Angle : 0.484 3.832 22692 Z= 0.255 Chirality : 0.040 0.131 2532 Planarity : 0.003 0.026 2736 Dihedral : 9.163 50.915 2904 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.28 % Allowed : 15.70 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.19), residues: 1872 helix: 3.64 (0.13), residues: 1284 sheet: 2.16 (0.56), residues: 132 loop : -1.32 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 79 HIS 0.002 0.001 HIS K 75 PHE 0.010 0.001 PHE H 33 TYR 0.016 0.002 TYR E 96 ARG 0.001 0.000 ARG B 233 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 1092) hydrogen bonds : angle 3.11985 ( 3240) SS BOND : bond 0.00208 ( 36) SS BOND : angle 0.97436 ( 72) covalent geometry : bond 0.00294 (16968) covalent geometry : angle 0.48214 (22620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 2.641 Fit side-chains REVERT: A 203 VAL cc_start: 0.6744 (OUTLIER) cc_final: 0.6368 (m) REVERT: J 94 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7773 (tp) REVERT: J 220 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.7917 (tt) REVERT: B 94 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7671 (tp) REVERT: C 94 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7763 (tp) REVERT: C 220 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.7918 (tt) REVERT: E 94 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7672 (tp) REVERT: F 94 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7768 (tp) REVERT: F 220 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.7923 (tt) REVERT: G 94 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7775 (tp) REVERT: G 220 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.7921 (tt) REVERT: I 94 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7690 (tp) REVERT: L 94 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7665 (tp) outliers start: 40 outliers final: 19 residues processed: 222 average time/residue: 1.9180 time to fit residues: 497.4468 Evaluate side-chains 214 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 103 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 133 optimal weight: 0.1980 chunk 55 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS K 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128097 restraints weight = 43677.989| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.70 r_work: 0.3437 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17004 Z= 0.174 Angle : 0.547 4.461 22692 Z= 0.288 Chirality : 0.042 0.139 2532 Planarity : 0.004 0.025 2736 Dihedral : 10.396 54.107 2904 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.23 % Allowed : 15.92 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.19), residues: 1872 helix: 3.43 (0.13), residues: 1296 sheet: 2.10 (0.57), residues: 132 loop : -1.29 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 79 HIS 0.005 0.001 HIS C 75 PHE 0.013 0.001 PHE H 33 TYR 0.017 0.002 TYR D 96 ARG 0.002 0.000 ARG I 69 Details of bonding type rmsd hydrogen bonds : bond 0.05697 ( 1092) hydrogen bonds : angle 3.26722 ( 3240) SS BOND : bond 0.00328 ( 36) SS BOND : angle 1.29854 ( 72) covalent geometry : bond 0.00439 (16968) covalent geometry : angle 0.54315 (22620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 2.548 Fit side-chains REVERT: J 94 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7616 (tp) REVERT: B 94 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7512 (tp) REVERT: C 94 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7619 (tp) REVERT: E 94 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7514 (tp) REVERT: F 94 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7625 (tp) REVERT: G 94 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7617 (tp) REVERT: I 94 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7504 (tp) REVERT: L 94 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7510 (tp) outliers start: 39 outliers final: 22 residues processed: 224 average time/residue: 1.8245 time to fit residues: 483.3589 Evaluate side-chains 224 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain K residue 75 HIS Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 HIS G 75 HIS H 75 HIS I 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.193010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.145862 restraints weight = 43219.526| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.47 r_work: 0.3501 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17004 Z= 0.108 Angle : 0.480 3.907 22692 Z= 0.255 Chirality : 0.039 0.130 2532 Planarity : 0.003 0.024 2736 Dihedral : 9.362 53.915 2904 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.40 % Allowed : 15.92 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.19), residues: 1872 helix: 3.57 (0.13), residues: 1284 sheet: 2.12 (0.55), residues: 132 loop : -1.42 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 79 HIS 0.006 0.001 HIS A 75 PHE 0.010 0.001 PHE H 33 TYR 0.017 0.002 TYR L 96 ARG 0.001 0.000 ARG L 69 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 1092) hydrogen bonds : angle 3.12445 ( 3240) SS BOND : bond 0.00167 ( 36) SS BOND : angle 0.91377 ( 72) covalent geometry : bond 0.00252 (16968) covalent geometry : angle 0.47787 (22620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 2.662 Fit side-chains REVERT: A 94 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7785 (tp) REVERT: A 203 VAL cc_start: 0.6779 (OUTLIER) cc_final: 0.6396 (m) REVERT: J 94 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7757 (tp) REVERT: B 94 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7651 (tp) REVERT: C 94 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7749 (tp) REVERT: D 203 VAL cc_start: 0.6791 (OUTLIER) cc_final: 0.6402 (m) REVERT: E 94 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7640 (tp) REVERT: F 94 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7749 (tp) REVERT: G 94 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7775 (tp) REVERT: H 203 VAL cc_start: 0.6772 (OUTLIER) cc_final: 0.6389 (m) REVERT: I 94 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7649 (tp) REVERT: K 203 VAL cc_start: 0.6753 (OUTLIER) cc_final: 0.6373 (m) REVERT: L 94 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7633 (tp) outliers start: 42 outliers final: 19 residues processed: 232 average time/residue: 2.1140 time to fit residues: 572.5340 Evaluate side-chains 228 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 75 HIS Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS K 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.189273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147357 restraints weight = 43022.129| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.30 r_work: 0.3523 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17004 Z= 0.112 Angle : 0.483 3.965 22692 Z= 0.256 Chirality : 0.039 0.136 2532 Planarity : 0.003 0.025 2736 Dihedral : 9.170 53.925 2904 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.71 % Allowed : 16.04 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.19), residues: 1872 helix: 3.60 (0.13), residues: 1284 sheet: 2.03 (0.54), residues: 132 loop : -1.47 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 79 HIS 0.003 0.001 HIS H 75 PHE 0.010 0.001 PHE H 33 TYR 0.020 0.002 TYR K 96 ARG 0.001 0.000 ARG L 69 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 1092) hydrogen bonds : angle 3.11166 ( 3240) SS BOND : bond 0.00175 ( 36) SS BOND : angle 0.92572 ( 72) covalent geometry : bond 0.00264 (16968) covalent geometry : angle 0.48093 (22620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 2.721 Fit side-chains REVERT: A 94 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7769 (tp) REVERT: A 203 VAL cc_start: 0.6760 (OUTLIER) cc_final: 0.6386 (m) REVERT: J 94 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7778 (tp) REVERT: B 94 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7618 (tp) REVERT: C 94 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7758 (tp) REVERT: D 94 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7789 (tp) REVERT: D 203 VAL cc_start: 0.6769 (OUTLIER) cc_final: 0.6388 (m) REVERT: E 94 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7613 (tp) REVERT: F 94 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7754 (tp) REVERT: G 94 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7769 (tp) REVERT: H 94 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7794 (tp) REVERT: H 203 VAL cc_start: 0.6772 (OUTLIER) cc_final: 0.6394 (m) REVERT: I 94 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7605 (tp) REVERT: K 94 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7786 (tp) REVERT: K 203 VAL cc_start: 0.6747 (OUTLIER) cc_final: 0.6372 (m) REVERT: L 94 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7608 (tp) outliers start: 30 outliers final: 14 residues processed: 212 average time/residue: 1.7871 time to fit residues: 442.8728 Evaluate side-chains 224 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain K residue 75 HIS Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 0.0770 chunk 123 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.187925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146142 restraints weight = 42866.146| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.28 r_work: 0.3527 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17004 Z= 0.115 Angle : 0.485 3.975 22692 Z= 0.257 Chirality : 0.039 0.134 2532 Planarity : 0.003 0.026 2736 Dihedral : 9.122 54.142 2904 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.60 % Allowed : 16.15 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.19), residues: 1872 helix: 3.61 (0.13), residues: 1284 sheet: 1.98 (0.53), residues: 132 loop : -1.52 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.006 0.001 HIS A 75 PHE 0.010 0.001 PHE H 33 TYR 0.020 0.002 TYR E 96 ARG 0.001 0.000 ARG I 69 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 1092) hydrogen bonds : angle 3.12459 ( 3240) SS BOND : bond 0.00185 ( 36) SS BOND : angle 0.94485 ( 72) covalent geometry : bond 0.00275 (16968) covalent geometry : angle 0.48252 (22620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 2.514 Fit side-chains REVERT: A 94 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7833 (tp) REVERT: A 203 VAL cc_start: 0.6816 (OUTLIER) cc_final: 0.6439 (m) REVERT: J 94 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7818 (tp) REVERT: B 94 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7662 (tp) REVERT: C 94 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7816 (tp) REVERT: D 94 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7847 (tp) REVERT: D 203 VAL cc_start: 0.6815 (OUTLIER) cc_final: 0.6432 (m) REVERT: E 94 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7662 (tp) REVERT: F 94 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7813 (tp) REVERT: G 94 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7830 (tp) REVERT: H 94 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7847 (tp) REVERT: H 203 VAL cc_start: 0.6819 (OUTLIER) cc_final: 0.6439 (m) REVERT: I 94 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7660 (tp) REVERT: K 94 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7848 (tp) REVERT: K 203 VAL cc_start: 0.6811 (OUTLIER) cc_final: 0.6437 (m) REVERT: L 94 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7653 (tp) outliers start: 28 outliers final: 12 residues processed: 210 average time/residue: 1.9184 time to fit residues: 482.3576 Evaluate side-chains 222 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 55 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 171 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS D 75 HIS H 75 HIS K 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.190221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148537 restraints weight = 42900.804| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.29 r_work: 0.3533 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17004 Z= 0.105 Angle : 0.469 3.967 22692 Z= 0.248 Chirality : 0.039 0.129 2532 Planarity : 0.003 0.027 2736 Dihedral : 8.827 54.260 2904 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.83 % Allowed : 15.92 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.19), residues: 1872 helix: 3.68 (0.13), residues: 1284 sheet: 1.98 (0.53), residues: 132 loop : -1.50 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 79 HIS 0.001 0.000 HIS J 75 PHE 0.009 0.001 PHE D 33 TYR 0.021 0.002 TYR J 96 ARG 0.001 0.000 ARG L 69 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 1092) hydrogen bonds : angle 3.09104 ( 3240) SS BOND : bond 0.00164 ( 36) SS BOND : angle 0.87420 ( 72) covalent geometry : bond 0.00248 (16968) covalent geometry : angle 0.46738 (22620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20435.12 seconds wall clock time: 350 minutes 15.53 seconds (21015.53 seconds total)