Starting phenix.real_space_refine on Tue Aug 26 02:25:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xh8_38344/08_2025/8xh8_38344_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xh8_38344/08_2025/8xh8_38344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xh8_38344/08_2025/8xh8_38344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xh8_38344/08_2025/8xh8_38344.map" model { file = "/net/cci-nas-00/data/ceres_data/8xh8_38344/08_2025/8xh8_38344_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xh8_38344/08_2025/8xh8_38344_trim.cif" } resolution = 2.72 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= 0.001 sd= 0.093 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 11100 2.51 5 N 2496 2.21 5 O 2676 1.98 5 H 15732 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32160 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "B" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "C" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "E" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "F" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "G" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "H" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "I" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "J" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "K" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "L" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2617 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "K" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Unusual residues: {'MC3': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 6.57, per 1000 atoms: 0.20 Number of scatterers: 32160 At special positions: 0 Unit cell: (100.386, 98.67, 150.15, 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 2676 8.00 N 2496 7.00 C 11100 6.00 H 15732 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.04 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.04 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 41 removed outlier: 4.147A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.844A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 46' Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 87 through 100 Processing helix chain 'A' and resid 197 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'B' and resid 21 through 41 removed outlier: 3.963A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.844A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 87 through 100 Processing helix chain 'B' and resid 197 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'C' and resid 21 through 41 removed outlier: 3.954A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.839A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 197 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'D' and resid 21 through 41 removed outlier: 3.963A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.838A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 87 through 100 Processing helix chain 'D' and resid 197 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 21 through 41 removed outlier: 3.959A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.833A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 87 through 100 Processing helix chain 'E' and resid 197 through 222 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.981A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.849A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 87 through 100 Processing helix chain 'F' and resid 197 through 222 Processing helix chain 'F' and resid 246 through 276 Processing helix chain 'G' and resid 21 through 41 removed outlier: 3.972A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.849A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 86 Processing helix chain 'G' and resid 87 through 100 Processing helix chain 'G' and resid 197 through 222 Processing helix chain 'G' and resid 246 through 276 Processing helix chain 'H' and resid 21 through 41 removed outlier: 3.946A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.838A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 46' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 86 Processing helix chain 'H' and resid 87 through 100 Processing helix chain 'H' and resid 197 through 222 Processing helix chain 'H' and resid 246 through 276 Processing helix chain 'I' and resid 21 through 41 removed outlier: 3.949A pdb=" N ILE I 25 " --> pdb=" O MET I 21 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.836A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 87 through 100 Processing helix chain 'I' and resid 197 through 222 Processing helix chain 'I' and resid 246 through 276 Processing helix chain 'J' and resid 21 through 41 removed outlier: 3.962A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 46 removed outlier: 3.839A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 41 through 46' Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 87 through 100 Processing helix chain 'J' and resid 197 through 222 Processing helix chain 'J' and resid 246 through 276 Processing helix chain 'K' and resid 21 through 41 removed outlier: 3.946A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.831A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 46' Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 86 Processing helix chain 'K' and resid 87 through 100 Processing helix chain 'K' and resid 197 through 222 Processing helix chain 'K' and resid 246 through 276 Processing helix chain 'L' and resid 21 through 41 removed outlier: 3.969A pdb=" N ILE L 25 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 removed outlier: 3.838A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 41 through 46' Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 86 Processing helix chain 'L' and resid 87 through 100 Processing helix chain 'L' and resid 197 through 222 Processing helix chain 'L' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.615A 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: 3.663A 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: 3.621A 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: 3.610A 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: 3.672A 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: 3.627A 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: 3.623A 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: 3.612A 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: 3.659A 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: 3.629A 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: 3.614A 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: 3.655A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3384 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: 6.71 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15696 1.04 - 1.23: 562 1.23 - 1.43: 6377 1.43 - 1.63: 9633 1.63 - 1.83: 204 Bond restraints: 32472 Sorted by residual: bond pdb=" C ARG F 246 " pdb=" O ARG F 246 " ideal model delta sigma weight residual 1.233 1.229 0.004 4.80e-03 4.34e+04 8.52e-01 bond pdb=" CB LYS I 238 " pdb=" CG LYS I 238 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.22e-01 bond pdb=" CB MET A 85 " pdb=" CG MET A 85 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.63e-01 bond pdb=" CB MET E 85 " pdb=" CG MET E 85 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.62e-01 bond pdb=" CB MET B 85 " pdb=" CG MET B 85 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.50e-01 ... (remaining 32467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 52104 1.11 - 2.21: 5391 2.21 - 3.32: 306 3.32 - 4.42: 75 4.42 - 5.53: 24 Bond angle restraints: 57900 Sorted by residual: angle pdb=" N GLU I 239 " pdb=" CA GLU I 239 " pdb=" C GLU I 239 " ideal model delta sigma weight residual 109.76 113.91 -4.15 1.64e+00 3.72e-01 6.39e+00 angle pdb=" N GLU C 239 " pdb=" CA GLU C 239 " pdb=" C GLU C 239 " ideal model delta sigma weight residual 109.76 113.61 -3.85 1.64e+00 3.72e-01 5.51e+00 angle pdb=" N GLU G 239 " pdb=" CA GLU G 239 " pdb=" C GLU G 239 " ideal model delta sigma weight residual 109.76 113.31 -3.55 1.64e+00 3.72e-01 4.68e+00 angle pdb=" N GLY C 42 " pdb=" CA GLY C 42 " pdb=" C GLY C 42 " ideal model delta sigma weight residual 113.24 115.91 -2.67 1.31e+00 5.83e-01 4.14e+00 angle pdb=" N GLY I 42 " pdb=" CA GLY I 42 " pdb=" C GLY I 42 " ideal model delta sigma weight residual 113.24 115.90 -2.66 1.31e+00 5.83e-01 4.13e+00 ... (remaining 57895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 13147 16.82 - 33.63: 1512 33.63 - 50.45: 719 50.45 - 67.26: 282 67.26 - 84.08: 24 Dihedral angle restraints: 15684 sinusoidal: 8532 harmonic: 7152 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 93.00 119.17 -26.17 1 1.00e+01 1.00e-02 9.84e+00 dihedral pdb=" CB CYS C 62 " pdb=" SG CYS C 62 " pdb=" SG CYS C 236 " pdb=" CB CYS C 236 " ideal model delta sinusoidal sigma weight residual 93.00 118.93 -25.93 1 1.00e+01 1.00e-02 9.66e+00 dihedral pdb=" CB CYS K 62 " pdb=" SG CYS K 62 " pdb=" SG CYS K 236 " pdb=" CB CYS K 236 " ideal model delta sinusoidal sigma weight residual 93.00 118.89 -25.89 1 1.00e+01 1.00e-02 9.63e+00 ... (remaining 15681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1615 0.036 - 0.073: 659 0.073 - 0.109: 233 0.109 - 0.146: 47 0.146 - 0.182: 2 Chirality restraints: 2556 Sorted by residual: chirality pdb=" CA LYS I 238 " pdb=" N LYS I 238 " pdb=" C LYS I 238 " pdb=" CB LYS I 238 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA ARG A 246 " pdb=" N ARG A 246 " pdb=" C ARG A 246 " pdb=" CB ARG A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA VAL C 225 " pdb=" N VAL C 225 " pdb=" C VAL C 225 " pdb=" CB VAL C 225 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 2553 not shown) Planarity restraints: 4548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 210 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C GLU L 210 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU L 210 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE L 211 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 210 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C GLU I 210 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU I 210 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE I 211 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 210 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C GLU E 210 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU E 210 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE E 211 " -0.010 2.00e-02 2.50e+03 ... (remaining 4545 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.38: 10102 2.38 - 2.93: 66756 2.93 - 3.49: 77678 3.49 - 4.04: 103677 4.04 - 4.60: 154347 Nonbonded interactions: 412560 Sorted by model distance: nonbonded pdb=" O SER L 245 " pdb=" HZ2 LYS L 250 " model vdw 1.820 2.450 nonbonded pdb=" O SER C 245 " pdb=" HZ2 LYS C 250 " model vdw 1.822 2.450 nonbonded pdb=" O SER D 245 " pdb=" HZ2 LYS D 250 " model vdw 1.827 2.450 nonbonded pdb=" O SER A 245 " pdb=" HZ2 LYS A 250 " model vdw 1.828 2.450 nonbonded pdb=" O SER J 245 " pdb=" HZ2 LYS J 250 " model vdw 1.828 2.450 ... (remaining 412555 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: 0.04 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 29.230 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.003 0.025 16776 Z= 0.164 Angle : 0.693 5.529 22524 Z= 0.396 Chirality : 0.044 0.182 2556 Planarity : 0.005 0.043 2700 Dihedral : 14.829 84.076 6192 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.34 % Allowed : 13.72 % Favored : 85.94 % 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 aren not related in a simple way. whole: 1.78 (0.17), residues: 1896 helix: 2.20 (0.13), residues: 1284 sheet: 1.11 (0.36), residues: 120 loop : -1.71 (0.22), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 69 TYR 0.014 0.002 TYR L 67 PHE 0.014 0.002 PHE E 53 TRP 0.003 0.001 TRP I 79 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00324 (16740) covalent geometry : angle 0.69017 (22452) SS BOND : bond 0.00533 ( 36) SS BOND : angle 1.28979 ( 72) hydrogen bonds : bond 0.13541 ( 1140) hydrogen bonds : angle 4.28868 ( 3384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8983 (m-40) cc_final: 0.8712 (m110) REVERT: A 210 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6865 (mm-30) REVERT: B 52 MET cc_start: 0.8774 (mmt) cc_final: 0.8474 (mmt) REVERT: B 210 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6706 (mm-30) REVERT: B 239 GLU cc_start: 0.8360 (tt0) cc_final: 0.8096 (tt0) REVERT: C 210 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6729 (mm-30) REVERT: D 63 ASN cc_start: 0.8931 (m-40) cc_final: 0.8714 (m110) REVERT: D 210 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6821 (mm-30) REVERT: D 224 SER cc_start: 0.8826 (p) cc_final: 0.8613 (t) REVERT: E 63 ASN cc_start: 0.8735 (m-40) cc_final: 0.8344 (m110) REVERT: E 210 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6755 (mm-30) REVERT: E 239 GLU cc_start: 0.8405 (tt0) cc_final: 0.8199 (tt0) REVERT: F 37 ILE cc_start: 0.7695 (mm) cc_final: 0.7437 (tp) REVERT: F 93 PHE cc_start: 0.6557 (t80) cc_final: 0.6265 (t80) REVERT: F 210 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6755 (mm-30) REVERT: G 37 ILE cc_start: 0.7658 (mm) cc_final: 0.7398 (tp) REVERT: G 93 PHE cc_start: 0.6523 (t80) cc_final: 0.6203 (t80) REVERT: G 210 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6777 (mm-30) REVERT: H 63 ASN cc_start: 0.8941 (m-40) cc_final: 0.8666 (m110) REVERT: H 210 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6840 (mm-30) REVERT: I 52 MET cc_start: 0.8846 (mmt) cc_final: 0.8486 (mmt) REVERT: I 63 ASN cc_start: 0.8781 (m-40) cc_final: 0.8395 (m110) REVERT: I 210 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6716 (mm-30) REVERT: I 239 GLU cc_start: 0.8173 (tt0) cc_final: 0.7955 (tt0) REVERT: J 93 PHE cc_start: 0.6606 (t80) cc_final: 0.6293 (t80) REVERT: J 210 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6739 (mm-30) REVERT: K 210 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6826 (mm-30) REVERT: L 63 ASN cc_start: 0.8887 (m-40) cc_final: 0.8523 (m110) REVERT: L 210 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6801 (mm-30) outliers start: 6 outliers final: 2 residues processed: 287 average time/residue: 0.9777 time to fit residues: 317.7288 Evaluate side-chains 253 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 251 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.177943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127389 restraints weight = 41939.962| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.40 r_work: 0.3303 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16776 Z= 0.190 Angle : 0.620 4.660 22524 Z= 0.338 Chirality : 0.043 0.140 2556 Planarity : 0.005 0.041 2700 Dihedral : 7.160 33.733 2679 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.96 % Allowed : 14.46 % Favored : 84.58 % 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 aren not related in a simple way. whole: 3.03 (0.18), residues: 1896 helix: 3.04 (0.13), residues: 1332 sheet: 1.62 (0.43), residues: 120 loop : -1.38 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 24 TYR 0.016 0.003 TYR L 67 PHE 0.010 0.001 PHE J 53 TRP 0.005 0.002 TRP C 79 HIS 0.003 0.001 HIS I 75 Details of bonding type rmsd covalent geometry : bond 0.00424 (16740) covalent geometry : angle 0.61511 (22452) SS BOND : bond 0.00687 ( 36) SS BOND : angle 1.52260 ( 72) hydrogen bonds : bond 0.08507 ( 1140) hydrogen bonds : angle 3.43742 ( 3384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.937 Fit side-chains REVERT: A 210 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6841 (mm-30) REVERT: B 52 MET cc_start: 0.8822 (mmt) cc_final: 0.8433 (mmt) REVERT: B 93 PHE cc_start: 0.6525 (t80) cc_final: 0.6210 (t80) REVERT: B 210 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6834 (mm-30) REVERT: B 239 GLU cc_start: 0.8579 (tt0) cc_final: 0.8328 (tt0) REVERT: C 210 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6766 (mm-30) REVERT: D 210 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6885 (mm-30) REVERT: E 93 PHE cc_start: 0.6596 (t80) cc_final: 0.6321 (t80) REVERT: E 210 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6867 (mm-30) REVERT: E 239 GLU cc_start: 0.8567 (tt0) cc_final: 0.8318 (tt0) REVERT: F 85 MET cc_start: 0.7935 (tpt) cc_final: 0.7645 (tpt) REVERT: F 93 PHE cc_start: 0.6590 (t80) cc_final: 0.6295 (t80) REVERT: F 210 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6851 (mm-30) REVERT: G 85 MET cc_start: 0.7965 (tpt) cc_final: 0.7675 (tpt) REVERT: G 93 PHE cc_start: 0.6585 (t80) cc_final: 0.6275 (t80) REVERT: G 210 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6798 (mm-30) REVERT: G 253 PHE cc_start: 0.8397 (t80) cc_final: 0.8190 (t80) REVERT: H 210 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6878 (mm-30) REVERT: I 52 MET cc_start: 0.8882 (mmt) cc_final: 0.8448 (mmt) REVERT: I 210 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6867 (mm-30) REVERT: I 239 GLU cc_start: 0.8492 (tt0) cc_final: 0.8237 (tt0) REVERT: J 93 PHE cc_start: 0.6683 (t80) cc_final: 0.6380 (t80) REVERT: J 210 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6786 (mm-30) REVERT: K 210 GLU cc_start: 0.7617 (mt-10) cc_final: 0.6865 (mm-30) REVERT: L 93 PHE cc_start: 0.6522 (t80) cc_final: 0.6234 (t80) REVERT: L 210 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6806 (mm-30) outliers start: 17 outliers final: 14 residues processed: 234 average time/residue: 0.9777 time to fit residues: 259.2384 Evaluate side-chains 239 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 230 GLU Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 230 GLU Chi-restraints excluded: chain L residue 230 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 207 ASN C 63 ASN C 207 ASN D 63 ASN D 207 ASN E 63 ASN E 207 ASN F 207 ASN G 63 ASN H 63 ASN H 207 ASN I 63 ASN I 207 ASN J 207 ASN K 207 ASN L 63 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.180305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131797 restraints weight = 42832.220| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.39 r_work: 0.3374 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16776 Z= 0.124 Angle : 0.497 4.360 22524 Z= 0.269 Chirality : 0.041 0.131 2556 Planarity : 0.003 0.031 2700 Dihedral : 5.600 33.914 2676 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.62 % Allowed : 15.76 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.71 (0.18), residues: 1896 helix: 3.56 (0.13), residues: 1332 sheet: 2.31 (0.43), residues: 120 loop : -1.31 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 69 TYR 0.011 0.001 TYR B 199 PHE 0.006 0.001 PHE I 71 TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00246 (16740) covalent geometry : angle 0.49583 (22452) SS BOND : bond 0.00204 ( 36) SS BOND : angle 0.73817 ( 72) hydrogen bonds : bond 0.06485 ( 1140) hydrogen bonds : angle 3.25518 ( 3384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 0.757 Fit side-chains REVERT: A 210 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6826 (mm-30) REVERT: B 52 MET cc_start: 0.8705 (mmt) cc_final: 0.8451 (mmt) REVERT: B 93 PHE cc_start: 0.6445 (t80) cc_final: 0.6129 (t80) REVERT: B 210 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6783 (mm-30) REVERT: B 239 GLU cc_start: 0.8573 (tt0) cc_final: 0.8277 (tt0) REVERT: C 210 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6714 (mm-30) REVERT: D 210 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6847 (mm-30) REVERT: E 52 MET cc_start: 0.8940 (mmt) cc_final: 0.8224 (mmt) REVERT: E 93 PHE cc_start: 0.6545 (t80) cc_final: 0.6234 (t80) REVERT: E 210 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6809 (mm-30) REVERT: E 239 GLU cc_start: 0.8539 (tt0) cc_final: 0.8313 (tt0) REVERT: F 93 PHE cc_start: 0.6500 (t80) cc_final: 0.6172 (t80) REVERT: F 210 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6822 (mm-30) REVERT: G 93 PHE cc_start: 0.6578 (t80) cc_final: 0.6216 (t80) REVERT: G 210 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6735 (mm-30) REVERT: G 253 PHE cc_start: 0.8270 (t80) cc_final: 0.8064 (t80) REVERT: H 210 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6852 (mm-30) REVERT: I 52 MET cc_start: 0.8783 (mmt) cc_final: 0.8460 (mmt) REVERT: I 93 PHE cc_start: 0.6523 (t80) cc_final: 0.6213 (t80) REVERT: I 210 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6789 (mm-30) REVERT: I 239 GLU cc_start: 0.8493 (tt0) cc_final: 0.8282 (tt0) REVERT: J 210 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6800 (mm-30) REVERT: J 239 GLU cc_start: 0.8701 (tt0) cc_final: 0.8496 (tt0) REVERT: K 210 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6860 (mm-30) REVERT: L 93 PHE cc_start: 0.6441 (t80) cc_final: 0.6142 (t80) REVERT: L 210 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6760 (mm-30) outliers start: 11 outliers final: 9 residues processed: 230 average time/residue: 1.1357 time to fit residues: 294.2245 Evaluate side-chains 229 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 220 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 116 optimal weight: 0.3980 chunk 191 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.175027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126652 restraints weight = 42477.705| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.39 r_work: 0.3313 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16776 Z= 0.163 Angle : 0.572 4.629 22524 Z= 0.302 Chirality : 0.043 0.144 2556 Planarity : 0.004 0.039 2700 Dihedral : 6.933 34.728 2676 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.36 % Allowed : 14.85 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.18), residues: 1896 helix: 3.49 (0.12), residues: 1332 sheet: 1.84 (0.43), residues: 120 loop : -1.43 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 206 TYR 0.013 0.002 TYR J 243 PHE 0.010 0.001 PHE L 53 TRP 0.004 0.002 TRP H 79 HIS 0.003 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00369 (16740) covalent geometry : angle 0.56761 (22452) SS BOND : bond 0.00593 ( 36) SS BOND : angle 1.31371 ( 72) hydrogen bonds : bond 0.07468 ( 1140) hydrogen bonds : angle 3.19345 ( 3384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.540 Fit side-chains REVERT: A 210 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6537 (mm-30) REVERT: B 52 MET cc_start: 0.8800 (mmt) cc_final: 0.8487 (mmt) REVERT: B 93 PHE cc_start: 0.6406 (t80) cc_final: 0.6109 (t80) REVERT: B 210 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6540 (mm-30) REVERT: C 210 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6617 (mm-30) REVERT: D 210 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6534 (mm-30) REVERT: E 52 MET cc_start: 0.9039 (mmt) cc_final: 0.8308 (mmt) REVERT: E 93 PHE cc_start: 0.6500 (t80) cc_final: 0.6227 (t80) REVERT: E 210 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6535 (mm-30) REVERT: E 239 GLU cc_start: 0.8559 (tt0) cc_final: 0.8338 (tt0) REVERT: F 93 PHE cc_start: 0.6544 (t80) cc_final: 0.6241 (t80) REVERT: F 210 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6643 (mm-30) REVERT: G 210 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6576 (mm-30) REVERT: H 210 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6571 (mm-30) REVERT: I 52 MET cc_start: 0.8868 (mmt) cc_final: 0.8484 (mmt) REVERT: I 93 PHE cc_start: 0.6512 (t80) cc_final: 0.6221 (t80) REVERT: I 210 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6558 (mm-30) REVERT: I 239 GLU cc_start: 0.8541 (tt0) cc_final: 0.8281 (tt0) REVERT: J 43 GLU cc_start: 0.7608 (tt0) cc_final: 0.7343 (tt0) REVERT: J 210 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6622 (mm-30) REVERT: K 210 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6569 (mm-30) REVERT: L 93 PHE cc_start: 0.6409 (t80) cc_final: 0.6131 (t80) REVERT: L 210 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6568 (mm-30) outliers start: 24 outliers final: 17 residues processed: 228 average time/residue: 0.9402 time to fit residues: 243.8965 Evaluate side-chains 234 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 230 GLU Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 45 optimal weight: 0.8980 chunk 123 optimal weight: 0.0270 chunk 23 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 176 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.179081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131479 restraints weight = 42473.466| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.40 r_work: 0.3380 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16776 Z= 0.112 Angle : 0.479 4.421 22524 Z= 0.256 Chirality : 0.040 0.121 2556 Planarity : 0.003 0.029 2700 Dihedral : 5.633 34.234 2676 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.74 % Allowed : 15.76 % Favored : 83.50 % 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 aren not related in a simple way. whole: 3.94 (0.18), residues: 1896 helix: 3.75 (0.12), residues: 1332 sheet: 2.26 (0.41), residues: 120 loop : -1.25 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 24 TYR 0.009 0.001 TYR A 67 PHE 0.005 0.001 PHE K 33 TRP 0.002 0.001 TRP H 79 HIS 0.002 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00214 (16740) covalent geometry : angle 0.47813 (22452) SS BOND : bond 0.00145 ( 36) SS BOND : angle 0.64177 ( 72) hydrogen bonds : bond 0.05868 ( 1140) hydrogen bonds : angle 3.13323 ( 3384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 0.767 Fit side-chains REVERT: A 210 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6611 (mm-30) REVERT: B 52 MET cc_start: 0.8710 (mmt) cc_final: 0.8365 (mmt) REVERT: B 93 PHE cc_start: 0.6457 (t80) cc_final: 0.6181 (t80) REVERT: B 210 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6584 (mm-30) REVERT: B 239 GLU cc_start: 0.8533 (tt0) cc_final: 0.8297 (tt0) REVERT: C 43 GLU cc_start: 0.7516 (tt0) cc_final: 0.7224 (tt0) REVERT: C 210 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6671 (mm-30) REVERT: D 95 THR cc_start: 0.6567 (m) cc_final: 0.6340 (m) REVERT: D 210 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6611 (mm-30) REVERT: E 52 MET cc_start: 0.8963 (mmt) cc_final: 0.8293 (mmt) REVERT: E 210 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6577 (mm-30) REVERT: E 239 GLU cc_start: 0.8518 (tt0) cc_final: 0.8286 (tt0) REVERT: F 93 PHE cc_start: 0.6608 (t80) cc_final: 0.6292 (t80) REVERT: F 210 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6637 (mm-30) REVERT: G 210 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6595 (mm-30) REVERT: H 210 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6621 (mm-30) REVERT: I 52 MET cc_start: 0.8747 (mmt) cc_final: 0.8405 (mmt) REVERT: I 210 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6582 (mm-30) REVERT: I 239 GLU cc_start: 0.8536 (tt0) cc_final: 0.8257 (tt0) REVERT: J 43 GLU cc_start: 0.7563 (tt0) cc_final: 0.7297 (tt0) REVERT: J 210 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6630 (mm-30) REVERT: K 210 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6617 (mm-30) REVERT: L 210 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6599 (mm-30) outliers start: 13 outliers final: 12 residues processed: 215 average time/residue: 1.0198 time to fit residues: 248.1291 Evaluate side-chains 217 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 187 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 0.0870 chunk 97 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN C 75 HIS C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 75 HIS J 207 ASN K 207 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.176909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129028 restraints weight = 42470.310| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.37 r_work: 0.3344 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16776 Z= 0.130 Angle : 0.520 4.517 22524 Z= 0.273 Chirality : 0.041 0.138 2556 Planarity : 0.004 0.035 2700 Dihedral : 6.172 34.070 2676 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.13 % Allowed : 15.99 % Favored : 82.88 % 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 aren not related in a simple way. whole: 3.89 (0.18), residues: 1896 helix: 3.76 (0.12), residues: 1332 sheet: 1.90 (0.42), residues: 120 loop : -1.32 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 206 TYR 0.012 0.002 TYR J 243 PHE 0.009 0.001 PHE D 53 TRP 0.003 0.001 TRP J 79 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00278 (16740) covalent geometry : angle 0.51794 (22452) SS BOND : bond 0.00409 ( 36) SS BOND : angle 0.97633 ( 72) hydrogen bonds : bond 0.06358 ( 1140) hydrogen bonds : angle 3.05336 ( 3384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.772 Fit side-chains REVERT: A 210 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6506 (mm-30) REVERT: B 52 MET cc_start: 0.8761 (mmt) cc_final: 0.8425 (mmt) REVERT: B 210 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6510 (mm-30) REVERT: C 43 GLU cc_start: 0.7595 (tt0) cc_final: 0.7312 (tt0) REVERT: C 210 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6549 (mm-30) REVERT: D 210 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6505 (mm-30) REVERT: E 52 MET cc_start: 0.8981 (mmt) cc_final: 0.8398 (mmt) REVERT: E 210 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6484 (mm-30) REVERT: E 239 GLU cc_start: 0.8511 (tt0) cc_final: 0.8252 (tt0) REVERT: F 210 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6580 (mm-30) REVERT: G 210 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6531 (mm-30) REVERT: H 210 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6520 (mm-30) REVERT: I 52 MET cc_start: 0.8757 (mmt) cc_final: 0.8406 (mmt) REVERT: I 210 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6532 (mm-30) REVERT: J 43 GLU cc_start: 0.7594 (tt0) cc_final: 0.7331 (tt0) REVERT: J 210 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6601 (mm-30) REVERT: K 210 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6515 (mm-30) REVERT: L 210 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6529 (mm-30) outliers start: 20 outliers final: 17 residues processed: 202 average time/residue: 1.1705 time to fit residues: 266.3535 Evaluate side-chains 213 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 230 GLU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 230 GLU Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 156 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 170 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.175476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127313 restraints weight = 42583.386| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.37 r_work: 0.3314 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16776 Z= 0.143 Angle : 0.546 4.527 22524 Z= 0.287 Chirality : 0.042 0.139 2556 Planarity : 0.004 0.040 2700 Dihedral : 6.682 34.633 2676 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.13 % Allowed : 15.70 % Favored : 83.16 % 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 aren not related in a simple way. whole: 3.84 (0.18), residues: 1896 helix: 3.72 (0.12), residues: 1332 sheet: 2.14 (0.44), residues: 120 loop : -1.42 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 206 TYR 0.011 0.002 TYR C 243 PHE 0.009 0.001 PHE F 53 TRP 0.003 0.001 TRP D 79 HIS 0.006 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00316 (16740) covalent geometry : angle 0.54339 (22452) SS BOND : bond 0.00489 ( 36) SS BOND : angle 1.11915 ( 72) hydrogen bonds : bond 0.06738 ( 1140) hydrogen bonds : angle 3.05766 ( 3384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.831 Fit side-chains REVERT: A 210 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6456 (mm-30) REVERT: B 52 MET cc_start: 0.8799 (mmt) cc_final: 0.8418 (mmt) REVERT: B 210 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6477 (mm-30) REVERT: C 43 GLU cc_start: 0.7615 (tt0) cc_final: 0.7342 (tt0) REVERT: C 210 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6540 (mm-30) REVERT: D 210 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6459 (mm-30) REVERT: E 210 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6446 (mm-30) REVERT: E 239 GLU cc_start: 0.8535 (tt0) cc_final: 0.8258 (tt0) REVERT: F 210 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6563 (mm-30) REVERT: G 210 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6526 (mm-30) REVERT: H 210 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6467 (mm-30) REVERT: I 52 MET cc_start: 0.8812 (mmt) cc_final: 0.8427 (mmt) REVERT: I 210 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6537 (mm-30) REVERT: J 43 GLU cc_start: 0.7648 (tt0) cc_final: 0.7387 (tt0) REVERT: J 210 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6582 (mm-30) REVERT: K 210 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6462 (mm-30) REVERT: L 210 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6483 (mm-30) outliers start: 20 outliers final: 15 residues processed: 199 average time/residue: 1.0592 time to fit residues: 238.0160 Evaluate side-chains 207 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 230 GLU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 230 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 90 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 75 HIS G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.176831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.127640 restraints weight = 42240.294| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.43 r_work: 0.3318 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16776 Z= 0.134 Angle : 0.527 4.509 22524 Z= 0.278 Chirality : 0.042 0.135 2556 Planarity : 0.004 0.041 2700 Dihedral : 6.505 34.545 2676 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.96 % Allowed : 15.82 % Favored : 83.22 % 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 aren not related in a simple way. whole: 3.94 (0.18), residues: 1896 helix: 3.79 (0.12), residues: 1332 sheet: 2.08 (0.44), residues: 120 loop : -1.35 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 206 TYR 0.012 0.002 TYR C 243 PHE 0.009 0.001 PHE L 53 TRP 0.003 0.001 TRP D 79 HIS 0.002 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00289 (16740) covalent geometry : angle 0.52462 (22452) SS BOND : bond 0.00410 ( 36) SS BOND : angle 1.04438 ( 72) hydrogen bonds : bond 0.06463 ( 1140) hydrogen bonds : angle 3.05329 ( 3384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.741 Fit side-chains REVERT: A 210 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6637 (mm-30) REVERT: B 52 MET cc_start: 0.8860 (mmt) cc_final: 0.8448 (mmt) REVERT: B 210 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6710 (mm-30) REVERT: C 43 GLU cc_start: 0.7707 (tt0) cc_final: 0.7486 (tt0) REVERT: C 210 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6815 (mm-30) REVERT: D 210 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6609 (mm-30) REVERT: E 210 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6690 (mm-30) REVERT: F 210 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6771 (mm-30) REVERT: G 210 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6761 (mm-30) REVERT: H 210 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6609 (mm-30) REVERT: I 52 MET cc_start: 0.8884 (mmt) cc_final: 0.8466 (mmt) REVERT: I 210 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6691 (mm-30) REVERT: J 43 GLU cc_start: 0.7769 (tt0) cc_final: 0.7526 (tt0) REVERT: J 210 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6792 (mm-30) REVERT: K 210 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6610 (mm-30) REVERT: L 210 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6688 (mm-30) outliers start: 17 outliers final: 16 residues processed: 195 average time/residue: 1.0383 time to fit residues: 228.4499 Evaluate side-chains 206 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 181 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN C 207 ASN D 207 ASN F 75 HIS F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.178428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131867 restraints weight = 41342.306| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.20 r_work: 0.3351 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16776 Z= 0.126 Angle : 0.514 4.626 22524 Z= 0.271 Chirality : 0.041 0.135 2556 Planarity : 0.004 0.039 2700 Dihedral : 6.242 34.393 2676 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.96 % Allowed : 15.99 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.07 (0.18), residues: 1896 helix: 3.88 (0.12), residues: 1332 sheet: 2.34 (0.45), residues: 120 loop : -1.34 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 206 TYR 0.011 0.002 TYR F 243 PHE 0.008 0.001 PHE L 53 TRP 0.003 0.001 TRP D 79 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00267 (16740) covalent geometry : angle 0.51203 (22452) SS BOND : bond 0.00355 ( 36) SS BOND : angle 0.96068 ( 72) hydrogen bonds : bond 0.06134 ( 1140) hydrogen bonds : angle 3.01765 ( 3384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.707 Fit side-chains REVERT: A 210 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6578 (mm-30) REVERT: B 52 MET cc_start: 0.8838 (mmt) cc_final: 0.8494 (mmt) REVERT: B 210 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6645 (mm-30) REVERT: C 43 GLU cc_start: 0.7643 (tt0) cc_final: 0.7400 (tt0) REVERT: C 210 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6702 (mm-30) REVERT: D 210 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6524 (mm-30) REVERT: E 210 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6625 (mm-30) REVERT: F 210 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6694 (mm-30) REVERT: G 210 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6712 (mm-30) REVERT: H 210 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6583 (mm-30) REVERT: I 52 MET cc_start: 0.8852 (mmt) cc_final: 0.8504 (mmt) REVERT: I 210 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6640 (mm-30) REVERT: J 210 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6682 (mm-30) REVERT: K 210 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6557 (mm-30) REVERT: L 210 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6637 (mm-30) outliers start: 17 outliers final: 16 residues processed: 190 average time/residue: 0.9813 time to fit residues: 210.6068 Evaluate side-chains 203 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN D 207 ASN F 207 ASN G 207 ASN H 207 ASN K 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129568 restraints weight = 41535.090| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.16 r_work: 0.3349 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16776 Z= 0.149 Angle : 0.554 4.641 22524 Z= 0.292 Chirality : 0.042 0.142 2556 Planarity : 0.004 0.042 2700 Dihedral : 6.801 34.491 2676 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.96 % Allowed : 16.27 % Favored : 82.77 % 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 aren not related in a simple way. whole: 3.98 (0.18), residues: 1896 helix: 3.81 (0.12), residues: 1332 sheet: 2.34 (0.47), residues: 120 loop : -1.39 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 206 TYR 0.012 0.002 TYR G 243 PHE 0.010 0.001 PHE L 53 TRP 0.003 0.001 TRP D 79 HIS 0.004 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00335 (16740) covalent geometry : angle 0.55103 (22452) SS BOND : bond 0.00512 ( 36) SS BOND : angle 1.22510 ( 72) hydrogen bonds : bond 0.06687 ( 1140) hydrogen bonds : angle 3.02238 ( 3384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.674 Fit side-chains REVERT: A 210 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6643 (mm-30) REVERT: B 52 MET cc_start: 0.8877 (mmt) cc_final: 0.8463 (mmt) REVERT: B 210 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6681 (mm-30) REVERT: C 43 GLU cc_start: 0.7643 (tt0) cc_final: 0.7404 (tt0) REVERT: C 210 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6785 (mm-30) REVERT: D 210 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6588 (mm-30) REVERT: E 210 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6658 (mm-30) REVERT: F 210 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6740 (mm-30) REVERT: G 210 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6785 (mm-30) REVERT: H 210 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6651 (mm-30) REVERT: I 52 MET cc_start: 0.8890 (mmt) cc_final: 0.8471 (mmt) REVERT: I 210 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6706 (mm-30) REVERT: J 43 GLU cc_start: 0.7677 (tt0) cc_final: 0.7457 (tt0) REVERT: J 210 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6747 (mm-30) REVERT: K 85 MET cc_start: 0.7853 (tpt) cc_final: 0.7184 (tpt) REVERT: K 210 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6620 (mm-30) REVERT: L 210 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6678 (mm-30) outliers start: 17 outliers final: 17 residues processed: 202 average time/residue: 0.9416 time to fit residues: 215.3533 Evaluate side-chains 214 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 230 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN C 63 ASN C 207 ASN D 207 ASN F 63 ASN F 207 ASN G 63 ASN G 207 ASN H 207 ASN J 63 ASN K 207 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.178399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132320 restraints weight = 41515.227| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.16 r_work: 0.3357 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16776 Z= 0.124 Angle : 0.514 4.555 22524 Z= 0.273 Chirality : 0.041 0.135 2556 Planarity : 0.004 0.039 2700 Dihedral : 6.302 34.369 2676 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.91 % Allowed : 16.78 % Favored : 82.31 % 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 aren not related in a simple way. whole: 4.10 (0.18), residues: 1896 helix: 3.91 (0.12), residues: 1332 sheet: 2.40 (0.45), residues: 120 loop : -1.36 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 206 TYR 0.011 0.002 TYR C 243 PHE 0.008 0.001 PHE L 53 TRP 0.002 0.001 TRP D 79 HIS 0.002 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00263 (16740) covalent geometry : angle 0.51231 (22452) SS BOND : bond 0.00361 ( 36) SS BOND : angle 0.96594 ( 72) hydrogen bonds : bond 0.06102 ( 1140) hydrogen bonds : angle 3.00325 ( 3384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9168.63 seconds wall clock time: 155 minutes 30.60 seconds (9330.60 seconds total)