Starting phenix.real_space_refine on Fri Mar 6 16:59:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xki_33254/03_2026/7xki_33254_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xki_33254/03_2026/7xki_33254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xki_33254/03_2026/7xki_33254_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xki_33254/03_2026/7xki_33254_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xki_33254/03_2026/7xki_33254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xki_33254/03_2026/7xki_33254.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 156 5.16 5 C 10836 2.51 5 N 2544 2.21 5 O 2748 1.98 5 H 15996 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32280 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "B" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "C" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "D" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "E" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "F" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "G" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "H" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "I" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "J" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "K" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "L" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2663 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {'MC3': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'MC3:plan-1': 4, 'MC3:plan-2': 4} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 5.97, per 1000 atoms: 0.18 Number of scatterers: 32280 At special positions: 0 Unit cell: (97.1568, 99.1809, 147.759, 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 2748 8.00 N 2544 7.00 C 10836 6.00 H 15996 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 B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " 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: 2.52 Conformation dependent library (CDL) restraints added in 911.3 milliseconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 12 sheets defined 75.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 4.057A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.581A pdb=" N ALA A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.580A pdb=" N CYS A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 195 through 221 Processing helix chain 'A' and resid 246 through 276 removed outlier: 3.652A pdb=" N LYS A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 42 removed outlier: 3.977A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.562A pdb=" N ALA B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 removed outlier: 3.516A pdb=" N TYR B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'B' and resid 246 through 276 removed outlier: 3.706A pdb=" N LYS B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 41 removed outlier: 4.014A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.581A pdb=" N ALA C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.517A pdb=" N TYR C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 195 through 221 Processing helix chain 'C' and resid 246 through 276 removed outlier: 3.669A pdb=" N LYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 42 removed outlier: 4.053A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 47 Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.570A pdb=" N ALA D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.630A pdb=" N CYS D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 101 Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 removed outlier: 3.702A pdb=" N LYS D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 42 removed outlier: 4.022A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.533A pdb=" N ALA E 65 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 removed outlier: 3.519A pdb=" N TYR E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 101 Processing helix chain 'E' and resid 195 through 221 Processing helix chain 'E' and resid 246 through 276 removed outlier: 3.713A pdb=" N LYS E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 41 removed outlier: 3.971A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 removed outlier: 3.577A pdb=" N ALA F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 removed outlier: 3.521A pdb=" N TYR F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 Processing helix chain 'F' and resid 195 through 221 Processing helix chain 'F' and resid 246 through 276 removed outlier: 3.674A pdb=" N LYS F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 41 removed outlier: 4.102A pdb=" N ARG G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 47 Processing helix chain 'G' and resid 61 through 71 removed outlier: 3.539A pdb=" N ALA G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 removed outlier: 3.631A pdb=" N CYS G 87 " --> pdb=" O ILE G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 101 Processing helix chain 'G' and resid 195 through 221 Processing helix chain 'G' and resid 246 through 276 removed outlier: 3.663A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 41 removed outlier: 4.066A pdb=" N ARG H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 47 Processing helix chain 'H' and resid 61 through 71 removed outlier: 3.529A pdb=" N ALA H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 87 removed outlier: 3.624A pdb=" N CYS H 87 " --> pdb=" O ILE H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 101 Processing helix chain 'H' and resid 195 through 222 Processing helix chain 'H' and resid 246 through 276 removed outlier: 3.693A pdb=" N LYS H 250 " --> pdb=" O ARG H 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 41 removed outlier: 3.851A pdb=" N ILE I 25 " --> pdb=" O MET I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 47 Processing helix chain 'I' and resid 61 through 71 removed outlier: 3.525A pdb=" N ALA I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 86 removed outlier: 3.508A pdb=" N TYR I 78 " --> pdb=" O SER I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 101 Processing helix chain 'I' and resid 195 through 221 Processing helix chain 'I' and resid 246 through 276 removed outlier: 3.662A pdb=" N LYS I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 41 removed outlier: 4.012A pdb=" N ARG J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 47 Processing helix chain 'J' and resid 61 through 71 removed outlier: 3.593A pdb=" N ALA J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 87 removed outlier: 3.505A pdb=" N TYR J 78 " --> pdb=" O SER J 74 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS J 87 " --> pdb=" O ILE J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 101 Processing helix chain 'J' and resid 195 through 221 Processing helix chain 'J' and resid 246 through 276 removed outlier: 3.697A pdb=" N LYS J 250 " --> pdb=" O ARG J 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 41 removed outlier: 3.926A pdb=" N ARG K 24 " --> pdb=" O THR K 20 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 47 removed outlier: 3.545A pdb=" N ASP K 47 " --> pdb=" O THR K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 71 removed outlier: 3.583A pdb=" N ALA K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 87 removed outlier: 3.506A pdb=" N TYR K 78 " --> pdb=" O SER K 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS K 87 " --> pdb=" O ILE K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 101 Processing helix chain 'K' and resid 195 through 221 Processing helix chain 'K' and resid 246 through 276 removed outlier: 3.690A pdb=" N LYS K 250 " --> pdb=" O ARG K 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 41 removed outlier: 4.212A pdb=" N ARG L 24 " --> pdb=" O THR L 20 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE L 25 " --> pdb=" O MET L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 47 Processing helix chain 'L' and resid 61 through 71 removed outlier: 3.567A pdb=" N ALA L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 87 removed outlier: 3.515A pdb=" N TYR L 78 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS L 87 " --> pdb=" O ILE L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 101 Processing helix chain 'L' and resid 195 through 221 Processing helix chain 'L' and resid 246 through 276 removed outlier: 3.709A pdb=" N LYS L 250 " --> pdb=" O ARG L 246 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.901A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.927A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.908A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.915A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.918A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.905A pdb=" N VAL F 54 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.888A pdb=" N VAL G 54 " --> pdb=" O TYR G 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.915A pdb=" N VAL H 54 " --> pdb=" O TYR H 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 removed outlier: 3.911A pdb=" N VAL I 54 " --> pdb=" O TYR I 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 removed outlier: 3.908A pdb=" N VAL J 54 " --> pdb=" O TYR J 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 removed outlier: 3.915A 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: 3.911A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3414 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: 7.21 Time building geometry restraints manager: 3.59 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: 15960 1.03 - 1.23: 192 1.23 - 1.43: 6840 1.43 - 1.62: 9420 1.62 - 1.82: 204 Bond restraints: 32616 Sorted by residual: bond pdb=" N LYS G 238 " pdb=" CA LYS G 238 " ideal model delta sigma weight residual 1.471 1.456 0.014 1.74e-02 3.30e+03 6.66e-01 bond pdb=" N LYS E 238 " pdb=" CA LYS E 238 " ideal model delta sigma weight residual 1.471 1.457 0.014 1.74e-02 3.30e+03 6.44e-01 bond pdb=" N LYS I 238 " pdb=" CA LYS I 238 " ideal model delta sigma weight residual 1.471 1.457 0.014 1.74e-02 3.30e+03 6.23e-01 bond pdb=" N LYS L 238 " pdb=" CA LYS L 238 " ideal model delta sigma weight residual 1.471 1.457 0.014 1.74e-02 3.30e+03 6.20e-01 bond pdb=" N LYS C 238 " pdb=" CA LYS C 238 " ideal model delta sigma weight residual 1.471 1.457 0.014 1.74e-02 3.30e+03 6.06e-01 ... (remaining 32611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 53537 0.93 - 1.86: 4810 1.86 - 2.79: 113 2.79 - 3.72: 54 3.72 - 4.65: 10 Bond angle restraints: 58524 Sorted by residual: angle pdb=" C LYS C 238 " pdb=" CA LYS C 238 " pdb=" CB LYS C 238 " ideal model delta sigma weight residual 116.34 111.69 4.65 1.40e+00 5.10e-01 1.10e+01 angle pdb=" C LYS D 238 " pdb=" CA LYS D 238 " pdb=" CB LYS D 238 " ideal model delta sigma weight residual 116.34 111.74 4.60 1.40e+00 5.10e-01 1.08e+01 angle pdb=" C LYS H 238 " pdb=" CA LYS H 238 " pdb=" CB LYS H 238 " ideal model delta sigma weight residual 116.34 111.81 4.53 1.40e+00 5.10e-01 1.05e+01 angle pdb=" C LYS J 238 " pdb=" CA LYS J 238 " pdb=" CB LYS J 238 " ideal model delta sigma weight residual 116.34 111.82 4.52 1.40e+00 5.10e-01 1.04e+01 angle pdb=" C LYS L 238 " pdb=" CA LYS L 238 " pdb=" CB LYS L 238 " ideal model delta sigma weight residual 116.34 111.89 4.45 1.40e+00 5.10e-01 1.01e+01 ... (remaining 58519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14240 17.99 - 35.97: 982 35.97 - 53.96: 315 53.96 - 71.94: 27 71.94 - 89.93: 12 Dihedral angle restraints: 15576 sinusoidal: 8304 harmonic: 7272 Sorted by residual: dihedral pdb=" CB CYS I 62 " pdb=" SG CYS I 62 " pdb=" SG CYS I 236 " pdb=" CB CYS I 236 " ideal model delta sinusoidal sigma weight residual 93.00 125.71 -32.71 1 1.00e+01 1.00e-02 1.52e+01 dihedral pdb=" CB CYS L 62 " pdb=" SG CYS L 62 " pdb=" SG CYS L 236 " pdb=" CB CYS L 236 " ideal model delta sinusoidal sigma weight residual 93.00 125.58 -32.58 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS H 62 " pdb=" SG CYS H 62 " pdb=" SG CYS H 236 " pdb=" CB CYS H 236 " ideal model delta sinusoidal sigma weight residual 93.00 125.07 -32.07 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 15573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1701 0.027 - 0.054: 379 0.054 - 0.081: 396 0.081 - 0.109: 103 0.109 - 0.136: 25 Chirality restraints: 2604 Sorted by residual: 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 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE J 73 " pdb=" N ILE J 73 " pdb=" C ILE J 73 " pdb=" CB ILE J 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 2601 not shown) Planarity restraints: 4644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 246 " -0.015 5.00e-02 4.00e+02 2.34e-02 8.78e-01 pdb=" N PRO L 247 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO L 247 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 247 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 246 " 0.014 5.00e-02 4.00e+02 2.17e-02 7.55e-01 pdb=" N PRO I 247 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO I 247 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO I 247 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 246 " -0.014 5.00e-02 4.00e+02 2.16e-02 7.46e-01 pdb=" N PRO G 247 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO G 247 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO G 247 " -0.012 5.00e-02 4.00e+02 ... (remaining 4641 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2846 2.24 - 2.83: 67980 2.83 - 3.42: 76840 3.42 - 4.01: 103455 4.01 - 4.60: 157742 Nonbonded interactions: 408863 Sorted by model distance: nonbonded pdb=" O ILE B 73 " pdb=" HH TYR B 221 " model vdw 1.652 2.450 nonbonded pdb=" O ILE D 73 " pdb=" HH TYR D 221 " model vdw 1.656 2.450 nonbonded pdb=" O ILE E 73 " pdb=" HH TYR E 221 " model vdw 1.656 2.450 nonbonded pdb=" O ILE H 73 " pdb=" HH TYR H 221 " model vdw 1.659 2.450 nonbonded pdb=" O ILE F 73 " pdb=" HH TYR F 221 " model vdw 1.660 2.450 ... (remaining 408858 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 10.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.900 Find NCS groups from input model: 0.570 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.002 0.020 16656 Z= 0.099 Angle : 0.412 4.653 22524 Z= 0.226 Chirality : 0.038 0.136 2604 Planarity : 0.003 0.023 2748 Dihedral : 13.459 89.926 5928 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.17 (0.19), residues: 1944 helix: 4.78 (0.12), residues: 1332 sheet: 2.58 (0.39), residues: 120 loop : -0.68 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 77 TYR 0.005 0.001 TYR F 199 PHE 0.007 0.001 PHE L 256 TRP 0.002 0.001 TRP F 79 HIS 0.002 0.000 HIS J 274 Details of bonding type rmsd covalent geometry : bond 0.00206 (16620) covalent geometry : angle 0.40981 (22452) SS BOND : bond 0.00106 ( 36) SS BOND : angle 0.80380 ( 72) hydrogen bonds : bond 0.11530 ( 1171) hydrogen bonds : angle 3.61836 ( 3414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4497 (mmm) cc_final: 0.4025 (pmm) REVERT: B 21 MET cc_start: 0.4579 (mmm) cc_final: 0.4180 (pmm) REVERT: C 21 MET cc_start: 0.4535 (mmm) cc_final: 0.4153 (pmm) REVERT: D 21 MET cc_start: 0.4580 (mmm) cc_final: 0.4036 (pmm) REVERT: G 21 MET cc_start: 0.4691 (mmm) cc_final: 0.4327 (pmm) REVERT: H 21 MET cc_start: 0.4739 (mmm) cc_final: 0.4098 (pmm) REVERT: I 21 MET cc_start: 0.4363 (mmm) cc_final: 0.3753 (pmm) REVERT: L 21 MET cc_start: 0.4703 (mmm) cc_final: 0.3401 (pmm) REVERT: L 93 PHE cc_start: 0.7234 (t80) cc_final: 0.6978 (t80) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.2635 time to fit residues: 168.7361 Evaluate side-chains 232 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.209374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171851 restraints weight = 55637.672| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.02 r_work: 0.3866 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16656 Z= 0.118 Angle : 0.461 4.714 22524 Z= 0.244 Chirality : 0.038 0.123 2604 Planarity : 0.003 0.032 2748 Dihedral : 4.729 37.742 2364 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.72 % Allowed : 7.28 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.86 (0.19), residues: 1944 helix: 4.40 (0.12), residues: 1344 sheet: 2.73 (0.40), residues: 120 loop : -0.52 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 197 TYR 0.004 0.001 TYR K 199 PHE 0.020 0.001 PHE F 256 TRP 0.002 0.001 TRP H 79 HIS 0.003 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00269 (16620) covalent geometry : angle 0.46001 (22452) SS BOND : bond 0.00145 ( 36) SS BOND : angle 0.76206 ( 72) hydrogen bonds : bond 0.04412 ( 1171) hydrogen bonds : angle 3.24513 ( 3414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4851 (mmm) cc_final: 0.3789 (pmm) REVERT: B 21 MET cc_start: 0.5114 (mmm) cc_final: 0.4160 (pmm) REVERT: C 21 MET cc_start: 0.5021 (mmm) cc_final: 0.4023 (pmm) REVERT: D 21 MET cc_start: 0.5212 (mmm) cc_final: 0.4257 (pmm) REVERT: G 21 MET cc_start: 0.5255 (mmm) cc_final: 0.4398 (pmm) REVERT: H 21 MET cc_start: 0.5151 (mmm) cc_final: 0.4128 (pmm) REVERT: I 21 MET cc_start: 0.4973 (mmm) cc_final: 0.4015 (pmm) REVERT: L 21 MET cc_start: 0.5064 (mmm) cc_final: 0.3645 (pmm) REVERT: L 29 VAL cc_start: 0.8319 (t) cc_final: 0.8098 (p) REVERT: L 93 PHE cc_start: 0.7520 (t80) cc_final: 0.7249 (t80) outliers start: 31 outliers final: 24 residues processed: 236 average time/residue: 0.2322 time to fit residues: 86.9718 Evaluate side-chains 229 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 199 TYR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 68 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 130 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 100 optimal weight: 0.2980 overall best weight: 0.7962 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.206541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.160159 restraints weight = 56846.667| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.74 r_work: 0.3757 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16656 Z= 0.105 Angle : 0.438 4.978 22524 Z= 0.231 Chirality : 0.037 0.140 2604 Planarity : 0.003 0.024 2748 Dihedral : 4.292 37.956 2364 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.89 % Allowed : 9.78 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.85 (0.19), residues: 1944 helix: 4.37 (0.12), residues: 1344 sheet: 2.96 (0.41), residues: 120 loop : -0.50 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.004 0.001 TYR H 199 PHE 0.022 0.001 PHE C 256 TRP 0.002 0.001 TRP D 79 HIS 0.002 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00238 (16620) covalent geometry : angle 0.43662 (22452) SS BOND : bond 0.00153 ( 36) SS BOND : angle 0.65600 ( 72) hydrogen bonds : bond 0.04074 ( 1171) hydrogen bonds : angle 3.06253 ( 3414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4994 (mmm) cc_final: 0.3832 (pmm) REVERT: A 29 VAL cc_start: 0.8152 (t) cc_final: 0.7879 (p) REVERT: B 21 MET cc_start: 0.5208 (mmm) cc_final: 0.4142 (pmm) REVERT: C 21 MET cc_start: 0.5208 (mmm) cc_final: 0.4038 (pmm) REVERT: D 21 MET cc_start: 0.5400 (mmm) cc_final: 0.4429 (pmm) REVERT: E 21 MET cc_start: 0.4912 (mmt) cc_final: 0.3481 (pmm) REVERT: E 29 VAL cc_start: 0.7810 (t) cc_final: 0.7535 (p) REVERT: G 21 MET cc_start: 0.5437 (mmm) cc_final: 0.4398 (pmm) REVERT: H 21 MET cc_start: 0.5280 (mmm) cc_final: 0.4007 (pmm) REVERT: I 21 MET cc_start: 0.5273 (mmm) cc_final: 0.4095 (pmm) REVERT: K 29 VAL cc_start: 0.8084 (t) cc_final: 0.7772 (p) REVERT: L 21 MET cc_start: 0.5285 (mmm) cc_final: 0.3830 (pmm) REVERT: L 93 PHE cc_start: 0.7271 (t80) cc_final: 0.7048 (t80) outliers start: 16 outliers final: 14 residues processed: 218 average time/residue: 0.2352 time to fit residues: 82.9502 Evaluate side-chains 213 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 127 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.202027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155561 restraints weight = 57210.104| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.69 r_work: 0.3693 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16656 Z= 0.167 Angle : 0.489 4.820 22524 Z= 0.267 Chirality : 0.038 0.131 2604 Planarity : 0.004 0.032 2748 Dihedral : 5.326 35.262 2364 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.61 % Allowed : 10.78 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.35 (0.19), residues: 1944 helix: 3.94 (0.13), residues: 1344 sheet: 3.51 (0.46), residues: 120 loop : -0.75 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 77 TYR 0.005 0.001 TYR H 199 PHE 0.028 0.001 PHE I 256 TRP 0.002 0.001 TRP K 79 HIS 0.002 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00391 (16620) covalent geometry : angle 0.48736 (22452) SS BOND : bond 0.00219 ( 36) SS BOND : angle 0.85665 ( 72) hydrogen bonds : bond 0.05287 ( 1171) hydrogen bonds : angle 3.39124 ( 3414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4953 (mmm) cc_final: 0.3867 (pmm) REVERT: A 29 VAL cc_start: 0.8173 (t) cc_final: 0.7882 (p) REVERT: B 21 MET cc_start: 0.5288 (mmm) cc_final: 0.4228 (pmm) REVERT: C 21 MET cc_start: 0.5251 (mmm) cc_final: 0.4080 (pmm) REVERT: D 21 MET cc_start: 0.5386 (mmm) cc_final: 0.4440 (pmm) REVERT: G 21 MET cc_start: 0.5388 (mmm) cc_final: 0.4389 (pmm) REVERT: H 21 MET cc_start: 0.5251 (mmm) cc_final: 0.4012 (pmm) REVERT: I 21 MET cc_start: 0.5245 (mmm) cc_final: 0.4088 (pmm) REVERT: L 21 MET cc_start: 0.5326 (mmm) cc_final: 0.3900 (pmm) outliers start: 11 outliers final: 10 residues processed: 232 average time/residue: 0.2253 time to fit residues: 84.2717 Evaluate side-chains 217 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.202196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.156219 restraints weight = 56826.194| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.65 r_work: 0.3708 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16656 Z= 0.128 Angle : 0.459 5.294 22524 Z= 0.247 Chirality : 0.038 0.130 2604 Planarity : 0.003 0.030 2748 Dihedral : 4.847 37.871 2364 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.72 % Allowed : 11.33 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.40 (0.19), residues: 1944 helix: 3.96 (0.13), residues: 1344 sheet: 3.47 (0.45), residues: 120 loop : -0.65 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.005 0.001 TYR H 199 PHE 0.020 0.001 PHE L 256 TRP 0.002 0.001 TRP L 79 HIS 0.002 0.000 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00297 (16620) covalent geometry : angle 0.45791 (22452) SS BOND : bond 0.00216 ( 36) SS BOND : angle 0.75306 ( 72) hydrogen bonds : bond 0.04661 ( 1171) hydrogen bonds : angle 3.24051 ( 3414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4942 (mmm) cc_final: 0.3835 (pmm) REVERT: B 21 MET cc_start: 0.5225 (mmm) cc_final: 0.4185 (pmm) REVERT: C 21 MET cc_start: 0.5209 (mmm) cc_final: 0.4029 (pmm) REVERT: D 21 MET cc_start: 0.5218 (mmm) cc_final: 0.4195 (pmm) REVERT: E 29 VAL cc_start: 0.7713 (t) cc_final: 0.7418 (p) REVERT: G 21 MET cc_start: 0.5282 (mmm) cc_final: 0.4230 (pmm) REVERT: H 21 MET cc_start: 0.5141 (mmm) cc_final: 0.3921 (pmm) REVERT: I 21 MET cc_start: 0.5215 (mmm) cc_final: 0.4069 (pmm) REVERT: L 21 MET cc_start: 0.5349 (mmm) cc_final: 0.3953 (pmm) outliers start: 13 outliers final: 12 residues processed: 219 average time/residue: 0.2123 time to fit residues: 78.6254 Evaluate side-chains 216 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 204 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 168 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 115 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.201576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155619 restraints weight = 56608.339| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.63 r_work: 0.3702 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16656 Z= 0.130 Angle : 0.459 5.899 22524 Z= 0.247 Chirality : 0.038 0.136 2604 Planarity : 0.003 0.029 2748 Dihedral : 4.915 41.960 2364 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.89 % Allowed : 11.28 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.38 (0.19), residues: 1944 helix: 3.95 (0.13), residues: 1344 sheet: 3.49 (0.46), residues: 120 loop : -0.68 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.005 0.001 TYR C 199 PHE 0.022 0.001 PHE L 256 TRP 0.002 0.001 TRP K 79 HIS 0.002 0.000 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00302 (16620) covalent geometry : angle 0.45799 (22452) SS BOND : bond 0.00208 ( 36) SS BOND : angle 0.74548 ( 72) hydrogen bonds : bond 0.04681 ( 1171) hydrogen bonds : angle 3.23266 ( 3414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4945 (mmm) cc_final: 0.3881 (pmm) REVERT: B 21 MET cc_start: 0.5208 (mmm) cc_final: 0.4147 (pmm) REVERT: C 21 MET cc_start: 0.5086 (mmm) cc_final: 0.3909 (pmm) REVERT: D 21 MET cc_start: 0.5188 (mmm) cc_final: 0.4135 (pmm) REVERT: E 29 VAL cc_start: 0.7732 (t) cc_final: 0.7430 (p) REVERT: G 21 MET cc_start: 0.5251 (mmm) cc_final: 0.4186 (pmm) REVERT: H 21 MET cc_start: 0.5198 (mmm) cc_final: 0.3968 (pmm) REVERT: I 21 MET cc_start: 0.5286 (mmm) cc_final: 0.4148 (pmm) REVERT: K 29 VAL cc_start: 0.7999 (t) cc_final: 0.7657 (p) REVERT: L 21 MET cc_start: 0.5399 (mmm) cc_final: 0.4052 (pmm) outliers start: 16 outliers final: 11 residues processed: 229 average time/residue: 0.2067 time to fit residues: 78.7295 Evaluate side-chains 215 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 135 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.203582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157736 restraints weight = 56748.576| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.66 r_work: 0.3727 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16656 Z= 0.101 Angle : 0.443 6.742 22524 Z= 0.232 Chirality : 0.037 0.147 2604 Planarity : 0.003 0.029 2748 Dihedral : 4.459 39.207 2364 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.94 % Allowed : 11.67 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.65 (0.19), residues: 1944 helix: 4.15 (0.13), residues: 1344 sheet: 3.47 (0.46), residues: 120 loop : -0.54 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.005 0.001 TYR C 199 PHE 0.006 0.001 PHE L 33 TRP 0.001 0.001 TRP L 79 HIS 0.003 0.000 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00228 (16620) covalent geometry : angle 0.44178 (22452) SS BOND : bond 0.00192 ( 36) SS BOND : angle 0.64699 ( 72) hydrogen bonds : bond 0.04053 ( 1171) hydrogen bonds : angle 3.04197 ( 3414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.4965 (mmm) cc_final: 0.3904 (pmm) REVERT: A 29 VAL cc_start: 0.7932 (t) cc_final: 0.7599 (p) REVERT: B 21 MET cc_start: 0.5101 (mmm) cc_final: 0.4027 (pmm) REVERT: C 21 MET cc_start: 0.5118 (mmm) cc_final: 0.3938 (pmm) REVERT: D 21 MET cc_start: 0.5184 (mmm) cc_final: 0.4122 (pmm) REVERT: E 29 VAL cc_start: 0.7772 (t) cc_final: 0.7484 (p) REVERT: G 21 MET cc_start: 0.5131 (mmm) cc_final: 0.4075 (pmm) REVERT: H 21 MET cc_start: 0.5181 (mmm) cc_final: 0.3933 (pmm) REVERT: I 21 MET cc_start: 0.5267 (mmm) cc_final: 0.4132 (pmm) REVERT: L 21 MET cc_start: 0.5338 (mmm) cc_final: 0.4013 (pmm) outliers start: 17 outliers final: 12 residues processed: 228 average time/residue: 0.2042 time to fit residues: 78.0700 Evaluate side-chains 212 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 22 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.201794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155545 restraints weight = 57536.371| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.66 r_work: 0.3713 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16656 Z= 0.120 Angle : 0.456 5.554 22524 Z= 0.241 Chirality : 0.038 0.169 2604 Planarity : 0.003 0.028 2748 Dihedral : 4.657 40.459 2364 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.72 % Allowed : 11.94 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.56 (0.19), residues: 1944 helix: 4.08 (0.13), residues: 1344 sheet: 3.50 (0.46), residues: 120 loop : -0.61 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 77 TYR 0.005 0.001 TYR C 199 PHE 0.023 0.001 PHE C 256 TRP 0.001 0.001 TRP L 79 HIS 0.003 0.000 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00277 (16620) covalent geometry : angle 0.45529 (22452) SS BOND : bond 0.00204 ( 36) SS BOND : angle 0.69218 ( 72) hydrogen bonds : bond 0.04316 ( 1171) hydrogen bonds : angle 3.11616 ( 3414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5019 (mmm) cc_final: 0.3947 (pmm) REVERT: A 29 VAL cc_start: 0.7913 (t) cc_final: 0.7592 (p) REVERT: B 21 MET cc_start: 0.5159 (mmm) cc_final: 0.4047 (pmm) REVERT: C 21 MET cc_start: 0.5100 (mmm) cc_final: 0.3932 (pmm) REVERT: D 21 MET cc_start: 0.5182 (mmm) cc_final: 0.4112 (pmm) REVERT: D 29 VAL cc_start: 0.7998 (t) cc_final: 0.7780 (p) REVERT: E 29 VAL cc_start: 0.7725 (t) cc_final: 0.7425 (p) REVERT: G 21 MET cc_start: 0.5076 (mmm) cc_final: 0.4036 (pmm) REVERT: H 21 MET cc_start: 0.5131 (mmm) cc_final: 0.3881 (pmm) REVERT: I 21 MET cc_start: 0.5285 (mmm) cc_final: 0.4187 (pmm) REVERT: L 21 MET cc_start: 0.5366 (mmm) cc_final: 0.4076 (pmm) outliers start: 13 outliers final: 10 residues processed: 215 average time/residue: 0.2164 time to fit residues: 77.3685 Evaluate side-chains 208 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 181 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.202654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156444 restraints weight = 57288.496| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.65 r_work: 0.3722 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 16656 Z= 0.107 Angle : 0.452 7.203 22524 Z= 0.236 Chirality : 0.038 0.187 2604 Planarity : 0.003 0.028 2748 Dihedral : 4.509 40.329 2364 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.61 % Allowed : 12.22 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.65 (0.19), residues: 1944 helix: 4.15 (0.13), residues: 1344 sheet: 3.52 (0.46), residues: 120 loop : -0.56 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 77 TYR 0.005 0.001 TYR C 199 PHE 0.022 0.001 PHE C 256 TRP 0.001 0.001 TRP G 79 HIS 0.003 0.000 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00243 (16620) covalent geometry : angle 0.45131 (22452) SS BOND : bond 0.00200 ( 36) SS BOND : angle 0.65838 ( 72) hydrogen bonds : bond 0.04081 ( 1171) hydrogen bonds : angle 3.03991 ( 3414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5140 (mmm) cc_final: 0.4038 (pmm) REVERT: A 29 VAL cc_start: 0.7933 (t) cc_final: 0.7614 (p) REVERT: B 21 MET cc_start: 0.5185 (mmm) cc_final: 0.4093 (pmm) REVERT: C 21 MET cc_start: 0.4987 (mmm) cc_final: 0.3874 (pmm) REVERT: D 21 MET cc_start: 0.5203 (mmm) cc_final: 0.4147 (pmm) REVERT: E 29 VAL cc_start: 0.7769 (t) cc_final: 0.7472 (p) REVERT: G 21 MET cc_start: 0.5115 (mmm) cc_final: 0.4088 (pmm) REVERT: H 21 MET cc_start: 0.5029 (mmm) cc_final: 0.3775 (pmm) REVERT: I 21 MET cc_start: 0.5240 (mmm) cc_final: 0.4149 (pmm) REVERT: L 21 MET cc_start: 0.5399 (mmm) cc_final: 0.4083 (pmm) outliers start: 11 outliers final: 11 residues processed: 209 average time/residue: 0.2167 time to fit residues: 75.6333 Evaluate side-chains 207 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 26 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 48 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 84 optimal weight: 0.1980 chunk 151 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.204123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.157918 restraints weight = 57433.549| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.66 r_work: 0.3739 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16656 Z= 0.093 Angle : 0.440 7.888 22524 Z= 0.228 Chirality : 0.038 0.184 2604 Planarity : 0.003 0.026 2748 Dihedral : 4.332 42.391 2364 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.61 % Allowed : 12.28 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.82 (0.19), residues: 1944 helix: 4.28 (0.13), residues: 1344 sheet: 3.51 (0.46), residues: 120 loop : -0.49 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 77 TYR 0.005 0.001 TYR C 199 PHE 0.021 0.001 PHE I 256 TRP 0.002 0.000 TRP G 79 HIS 0.003 0.000 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00211 (16620) covalent geometry : angle 0.43935 (22452) SS BOND : bond 0.00177 ( 36) SS BOND : angle 0.60647 ( 72) hydrogen bonds : bond 0.03691 ( 1171) hydrogen bonds : angle 2.93501 ( 3414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.5142 (mmm) cc_final: 0.4040 (pmm) REVERT: A 29 VAL cc_start: 0.7916 (t) cc_final: 0.7603 (p) REVERT: B 21 MET cc_start: 0.5157 (mmm) cc_final: 0.4079 (pmm) REVERT: C 21 MET cc_start: 0.4980 (mmm) cc_final: 0.3855 (pmm) REVERT: D 21 MET cc_start: 0.5192 (mmm) cc_final: 0.4171 (pmm) REVERT: E 29 VAL cc_start: 0.7749 (t) cc_final: 0.7456 (p) REVERT: G 21 MET cc_start: 0.5051 (mmm) cc_final: 0.4013 (pmm) REVERT: H 21 MET cc_start: 0.5013 (mmm) cc_final: 0.3757 (pmm) REVERT: I 21 MET cc_start: 0.5181 (mmm) cc_final: 0.4145 (pmm) REVERT: K 29 VAL cc_start: 0.7981 (t) cc_final: 0.7720 (p) REVERT: L 21 MET cc_start: 0.5393 (mmm) cc_final: 0.4102 (pmm) outliers start: 11 outliers final: 10 residues processed: 206 average time/residue: 0.2076 time to fit residues: 72.2342 Evaluate side-chains 203 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 265 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4360 r_free = 0.4360 target = 0.201128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154961 restraints weight = 57752.253| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.66 r_work: 0.3710 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16656 Z= 0.131 Angle : 0.470 6.074 22524 Z= 0.249 Chirality : 0.038 0.178 2604 Planarity : 0.003 0.028 2748 Dihedral : 4.707 40.771 2364 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.56 % Allowed : 12.39 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.58 (0.19), residues: 1944 helix: 4.09 (0.13), residues: 1344 sheet: 3.53 (0.47), residues: 120 loop : -0.59 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 77 TYR 0.005 0.001 TYR H 199 PHE 0.022 0.001 PHE C 256 TRP 0.002 0.001 TRP E 79 HIS 0.003 0.000 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00308 (16620) covalent geometry : angle 0.46934 (22452) SS BOND : bond 0.00215 ( 36) SS BOND : angle 0.72671 ( 72) hydrogen bonds : bond 0.04368 ( 1171) hydrogen bonds : angle 3.12956 ( 3414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6774.99 seconds wall clock time: 115 minutes 34.21 seconds (6934.21 seconds total)