Starting phenix.real_space_refine on Fri May 30 01:47:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgf_38320/05_2025/8xgf_38320_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgf_38320/05_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_38320/05_2025/8xgf_38320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgf_38320/05_2025/8xgf_38320.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgf_38320/05_2025/8xgf_38320_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgf_38320/05_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-5687/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: 10.49, 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: 7.75 Conformation dependent library (CDL) restraints added in 2.2 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: 2.09 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: 10.33 Time building geometry restraints manager: 9.38 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: 0.15 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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.540 Extract box with map and model: 1.260 Check model and map are aligned: 0.250 Set scattering table: 0.350 Process input model: 55.910 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.790 ------------------------------------------------------------------------------- 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 : 2.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 1.7082 time to fit residues: 549.0163 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 : 2.498 ------------------------------------------------------------------------------- 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 = 0.142814 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: 4.11 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 : 2.496 Fit side-chains REVERT: L 239 GLU cc_start: 0.8574 (tt0) cc_final: 0.8365 (tt0) outliers start: 42 outliers final: 24 residues processed: 247 average time/residue: 1.7172 time to fit residues: 499.4912 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 : 2.287 ------------------------------------------------------------------------------- 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: 9.9990 chunk 70 optimal weight: 3.9990 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: 1.4988 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.197579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.150754 restraints weight = 43550.494| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.43 r_work: 0.3629 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1853 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= 0.123 Angle : 0.487 3.861 22692 Z= 0.254 Chirality : 0.040 0.130 2532 Planarity : 0.004 0.038 2736 Dihedral : 9.647 50.059 2904 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.28 % Allowed : 15.92 % Favored : 81.79 % 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: 3.71 (0.20), residues: 1872 helix: 3.68 (0.13), residues: 1284 sheet: 2.26 (0.59), residues: 132 loop : -1.43 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 79 HIS 0.003 0.001 HIS I 75 PHE 0.009 0.001 PHE F 33 TYR 0.007 0.001 TYR A 243 ARG 0.001 0.000 ARG L 233 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 1092) hydrogen bonds : angle 3.10812 ( 3240) SS BOND : bond 0.00196 ( 36) SS BOND : angle 0.97421 ( 72) covalent geometry : bond 0.00294 (16968) covalent geometry : angle 0.48491 (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 231 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 2.368 Fit side-chains REVERT: B 220 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.7946 (tt) REVERT: E 220 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.7936 (tt) REVERT: I 220 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7942 (tt) REVERT: L 220 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7943 (tt) outliers start: 40 outliers final: 28 residues processed: 219 average time/residue: 1.8201 time to fit residues: 464.3861 Evaluate side-chains 223 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 2.387 ------------------------------------------------------------------------------- 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 E residue 220 LEU 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 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: 0.8980 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.184397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138570 restraints weight = 43403.429| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.55 r_work: 0.3589 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2111 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= 0.113 Angle : 0.468 3.822 22692 Z= 0.246 Chirality : 0.039 0.130 2532 Planarity : 0.004 0.037 2736 Dihedral : 9.107 50.843 2904 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.28 % Allowed : 15.18 % 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: 3.69 (0.19), residues: 1872 helix: 3.66 (0.13), residues: 1284 sheet: 2.04 (0.56), residues: 132 loop : -1.36 (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 A 75 PHE 0.009 0.001 PHE C 33 TYR 0.007 0.001 TYR D 243 ARG 0.002 0.000 ARG I 24 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 1092) hydrogen bonds : angle 3.05755 ( 3240) SS BOND : bond 0.00173 ( 36) SS BOND : angle 0.94393 ( 72) covalent geometry : bond 0.00271 (16968) covalent geometry : angle 0.46600 (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 243 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 2.216 Fit side-chains outliers start: 40 outliers final: 32 residues processed: 231 average time/residue: 1.7646 time to fit residues: 477.4664 Evaluate side-chains 222 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 2.258 ------------------------------------------------------------------------------- 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 E residue 220 LEU 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 Chi-restraints excluded: chain L residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 157 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 HIS H 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.188280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141747 restraints weight = 43476.630| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.41 r_work: 0.3549 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2278 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= 0.087 Angle : 0.434 3.771 22692 Z= 0.228 Chirality : 0.038 0.123 2532 Planarity : 0.003 0.033 2736 Dihedral : 8.246 49.099 2904 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.40 % Allowed : 15.41 % Favored : 82.19 % 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: 4.06 (0.19), residues: 1872 helix: 3.86 (0.13), residues: 1272 sheet: 2.11 (0.55), residues: 132 loop : -0.80 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP F 79 HIS 0.001 0.000 HIS J 99 PHE 0.007 0.001 PHE G 33 TYR 0.016 0.001 TYR K 96 ARG 0.001 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 1092) hydrogen bonds : angle 2.99027 ( 3240) SS BOND : bond 0.00104 ( 36) SS BOND : angle 0.68487 ( 72) covalent geometry : bond 0.00193 (16968) covalent geometry : angle 0.43316 (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 243 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 2.741 Fit side-chains REVERT: A 203 VAL cc_start: 0.6704 (OUTLIER) cc_final: 0.6340 (m) REVERT: J 94 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7818 (tp) REVERT: J 220 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7900 (tt) REVERT: B 94 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7655 (tp) REVERT: C 94 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7802 (tp) REVERT: C 220 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7894 (tt) REVERT: D 203 VAL cc_start: 0.6742 (OUTLIER) cc_final: 0.6375 (m) REVERT: E 94 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7640 (tp) REVERT: F 94 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7799 (tp) REVERT: F 220 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7906 (tt) REVERT: G 94 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7803 (tp) REVERT: G 220 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7909 (tt) REVERT: H 203 VAL cc_start: 0.6732 (OUTLIER) cc_final: 0.6362 (m) REVERT: I 94 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7660 (tp) REVERT: K 203 VAL cc_start: 0.6754 (OUTLIER) cc_final: 0.6391 (m) REVERT: L 94 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7647 (tp) outliers start: 42 outliers final: 20 residues processed: 231 average time/residue: 1.7710 time to fit residues: 477.3758 Evaluate side-chains 222 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 2.231 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 78 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.191090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141874 restraints weight = 43604.818| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.67 r_work: 0.3450 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17004 Z= 0.175 Angle : 0.536 4.293 22692 Z= 0.283 Chirality : 0.041 0.137 2532 Planarity : 0.004 0.031 2736 Dihedral : 10.021 52.073 2904 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.34 % Allowed : 15.75 % Favored : 81.91 % 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: 3.60 (0.20), residues: 1872 helix: 3.57 (0.13), residues: 1284 sheet: 2.07 (0.57), residues: 132 loop : -1.35 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP K 79 HIS 0.005 0.001 HIS C 75 PHE 0.013 0.001 PHE A 33 TYR 0.015 0.002 TYR D 96 ARG 0.001 0.000 ARG E 233 Details of bonding type rmsd hydrogen bonds : bond 0.05520 ( 1092) hydrogen bonds : angle 3.20322 ( 3240) SS BOND : bond 0.00331 ( 36) SS BOND : angle 1.22877 ( 72) covalent geometry : bond 0.00443 (16968) covalent geometry : angle 0.53256 (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 239 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 2.269 Fit side-chains REVERT: J 94 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7702 (tp) REVERT: B 94 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7611 (tp) REVERT: C 94 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7711 (tp) REVERT: E 94 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7593 (tp) REVERT: F 94 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7686 (tp) REVERT: G 94 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7706 (tp) REVERT: I 94 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7618 (tp) REVERT: L 94 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7594 (tp) outliers start: 41 outliers final: 22 residues processed: 227 average time/residue: 1.7836 time to fit residues: 472.1903 Evaluate side-chains 216 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain L residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 103 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 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: 0.8980 chunk 95 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.191200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144228 restraints weight = 43263.688| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.42 r_work: 0.3487 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2751 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= 0.154 Angle : 0.525 4.185 22692 Z= 0.277 Chirality : 0.041 0.137 2532 Planarity : 0.004 0.027 2736 Dihedral : 9.968 54.224 2904 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.34 % Allowed : 16.27 % Favored : 81.39 % 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: 3.47 (0.19), residues: 1872 helix: 3.49 (0.13), residues: 1284 sheet: 2.00 (0.56), residues: 132 loop : -1.42 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 79 HIS 0.004 0.001 HIS C 75 PHE 0.011 0.001 PHE H 33 TYR 0.018 0.002 TYR K 96 ARG 0.002 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.05354 ( 1092) hydrogen bonds : angle 3.21936 ( 3240) SS BOND : bond 0.00269 ( 36) SS BOND : angle 1.20045 ( 72) covalent geometry : bond 0.00385 (16968) covalent geometry : angle 0.52161 (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 241 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 2.397 Fit side-chains REVERT: J 94 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7783 (tp) REVERT: B 94 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7656 (tp) REVERT: C 94 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7800 (tp) REVERT: E 94 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7652 (tp) REVERT: F 94 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7806 (tp) REVERT: G 94 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7793 (tp) REVERT: I 94 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7648 (tp) REVERT: L 94 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7643 (tp) outliers start: 41 outliers final: 24 residues processed: 229 average time/residue: 1.8131 time to fit residues: 488.5927 Evaluate side-chains 222 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 2.279 ------------------------------------------------------------------------------- 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 75 HIS 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 E residue 220 LEU 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 75 HIS 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 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=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: 0.8980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.188137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146245 restraints weight = 43020.427| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.29 r_work: 0.3525 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2792 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= 0.107 Angle : 0.476 3.905 22692 Z= 0.253 Chirality : 0.039 0.130 2532 Planarity : 0.003 0.024 2736 Dihedral : 9.270 53.960 2904 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.94 % Allowed : 16.32 % Favored : 81.74 % 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: 3.60 (0.19), residues: 1872 helix: 3.59 (0.13), residues: 1284 sheet: 2.09 (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 K 79 HIS 0.006 0.001 HIS A 75 PHE 0.009 0.001 PHE D 33 TYR 0.017 0.002 TYR F 96 ARG 0.001 0.000 ARG L 69 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 1092) hydrogen bonds : angle 3.11747 ( 3240) SS BOND : bond 0.00165 ( 36) SS BOND : angle 0.89303 ( 72) covalent geometry : bond 0.00249 (16968) covalent geometry : angle 0.47413 (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 230 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 2.213 Fit side-chains REVERT: A 94 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7809 (tp) REVERT: A 203 VAL cc_start: 0.6796 (OUTLIER) cc_final: 0.6416 (m) REVERT: J 94 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7810 (tp) REVERT: J 220 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.7955 (tt) REVERT: B 94 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7668 (tp) REVERT: C 94 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7775 (tp) REVERT: C 220 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.7952 (tt) REVERT: D 94 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7800 (tp) REVERT: D 203 VAL cc_start: 0.6800 (OUTLIER) cc_final: 0.6415 (m) REVERT: E 94 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7659 (tp) REVERT: F 94 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7775 (tp) REVERT: F 220 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.7963 (tt) REVERT: G 94 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7791 (tp) REVERT: G 220 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.7956 (tt) REVERT: H 94 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7800 (tp) REVERT: H 203 VAL cc_start: 0.6798 (OUTLIER) cc_final: 0.6418 (m) REVERT: I 94 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7671 (tp) REVERT: K 94 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7804 (tp) REVERT: K 203 VAL cc_start: 0.6776 (OUTLIER) cc_final: 0.6398 (m) REVERT: L 94 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7652 (tp) outliers start: 34 outliers final: 14 residues processed: 218 average time/residue: 1.7537 time to fit residues: 447.9991 Evaluate side-chains 228 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 2.318 ------------------------------------------------------------------------------- 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 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 75 HIS 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 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 75 HIS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 0.5980 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.192404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145306 restraints weight = 43174.127| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.47 r_work: 0.3496 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17004 Z= 0.123 Angle : 0.492 3.982 22692 Z= 0.260 Chirality : 0.039 0.132 2532 Planarity : 0.003 0.024 2736 Dihedral : 9.332 54.765 2904 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.40 % Allowed : 15.75 % 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: 3.56 (0.19), residues: 1872 helix: 3.58 (0.13), residues: 1284 sheet: 2.02 (0.54), residues: 132 loop : -1.49 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS D 75 PHE 0.011 0.001 PHE K 33 TYR 0.019 0.002 TYR K 96 ARG 0.001 0.000 ARG L 69 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 1092) hydrogen bonds : angle 3.14587 ( 3240) SS BOND : bond 0.00210 ( 36) SS BOND : angle 0.99851 ( 72) covalent geometry : bond 0.00297 (16968) covalent geometry : angle 0.48923 (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 238 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 2.461 Fit side-chains REVERT: A 94 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7782 (tp) REVERT: A 203 VAL cc_start: 0.6749 (OUTLIER) cc_final: 0.6371 (m) REVERT: J 94 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7814 (tp) REVERT: B 94 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7601 (tp) REVERT: C 94 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7798 (tp) REVERT: D 94 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7801 (tp) REVERT: D 203 VAL cc_start: 0.6753 (OUTLIER) cc_final: 0.6370 (m) REVERT: E 94 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7605 (tp) REVERT: F 94 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7798 (tp) REVERT: G 94 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7793 (tp) REVERT: H 94 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7798 (tp) REVERT: H 203 VAL cc_start: 0.6758 (OUTLIER) cc_final: 0.6381 (m) REVERT: I 94 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7603 (tp) REVERT: K 94 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7789 (tp) REVERT: K 203 VAL cc_start: 0.6739 (OUTLIER) cc_final: 0.6365 (m) REVERT: L 94 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7613 (tp) outliers start: 42 outliers final: 18 residues processed: 226 average time/residue: 1.6836 time to fit residues: 449.0706 Evaluate side-chains 229 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 2.458 ------------------------------------------------------------------------------- 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 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 E residue 220 LEU 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 75 HIS 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 Chi-restraints excluded: chain L residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.193728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146776 restraints weight = 43063.698| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.46 r_work: 0.3512 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2852 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= 0.101 Angle : 0.468 3.979 22692 Z= 0.248 Chirality : 0.039 0.130 2532 Planarity : 0.003 0.024 2736 Dihedral : 8.945 54.791 2904 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.94 % Allowed : 16.44 % Favored : 81.62 % 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: 3.63 (0.19), residues: 1872 helix: 3.65 (0.13), residues: 1284 sheet: 1.95 (0.53), residues: 132 loop : -1.48 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 79 HIS 0.009 0.001 HIS A 75 PHE 0.009 0.001 PHE K 33 TYR 0.021 0.002 TYR F 96 ARG 0.001 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 1092) hydrogen bonds : angle 3.09827 ( 3240) SS BOND : bond 0.00148 ( 36) SS BOND : angle 0.84894 ( 72) covalent geometry : bond 0.00232 (16968) covalent geometry : angle 0.46641 (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 228 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 2.532 Fit side-chains REVERT: A 94 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7777 (tp) REVERT: A 203 VAL cc_start: 0.6714 (OUTLIER) cc_final: 0.6352 (m) REVERT: J 94 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7795 (tp) REVERT: B 94 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7591 (tp) REVERT: C 94 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7792 (tp) REVERT: D 94 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7770 (tp) REVERT: D 203 VAL cc_start: 0.6723 (OUTLIER) cc_final: 0.6354 (m) REVERT: E 94 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7592 (tp) REVERT: F 94 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7782 (tp) REVERT: G 94 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7792 (tp) REVERT: H 94 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7771 (tp) REVERT: H 203 VAL cc_start: 0.6735 (OUTLIER) cc_final: 0.6371 (m) REVERT: I 94 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7594 (tp) REVERT: K 94 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7772 (tp) REVERT: K 203 VAL cc_start: 0.6703 (OUTLIER) cc_final: 0.6348 (m) REVERT: L 94 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7588 (tp) outliers start: 34 outliers final: 16 residues processed: 216 average time/residue: 1.8345 time to fit residues: 473.8262 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 : 2.424 ------------------------------------------------------------------------------- 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 E residue 220 LEU 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 75 HIS 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 Chi-restraints excluded: chain L residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 55 optimal weight: 4.9990 chunk 187 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.192170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.145039 restraints weight = 43126.904| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.46 r_work: 0.3492 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17004 Z= 0.129 Angle : 0.502 4.006 22692 Z= 0.265 Chirality : 0.040 0.133 2532 Planarity : 0.003 0.024 2736 Dihedral : 9.497 56.235 2904 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.00 % Allowed : 16.10 % Favored : 81.91 % 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: 3.55 (0.19), residues: 1872 helix: 3.58 (0.13), residues: 1284 sheet: 1.99 (0.54), residues: 132 loop : -1.50 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 79 HIS 0.003 0.001 HIS C 75 PHE 0.011 0.001 PHE D 33 TYR 0.020 0.002 TYR K 96 ARG 0.001 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 1092) hydrogen bonds : angle 3.15896 ( 3240) SS BOND : bond 0.00223 ( 36) SS BOND : angle 1.03285 ( 72) covalent geometry : bond 0.00316 (16968) covalent geometry : angle 0.49894 (22620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19018.46 seconds wall clock time: 325 minutes 52.43 seconds (19552.43 seconds total)