Starting phenix.real_space_refine on Thu May 29 21:02:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xh8_38344/05_2025/8xh8_38344_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xh8_38344/05_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_38344/05_2025/8xh8_38344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xh8_38344/05_2025/8xh8_38344.map" model { file = "/net/cci-nas-00/data/ceres_data/8xh8_38344/05_2025/8xh8_38344_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xh8_38344/05_2025/8xh8_38344_trim.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 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-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 13.31, per 1000 atoms: 0.41 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: 7.20 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.08 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: 10.15 Time building geometry restraints manager: 8.81 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.510 Extract box with map and model: 1.020 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 56.950 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.003 0.001 TRP I 79 HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE E 53 TYR 0.014 0.002 TYR L 67 ARG 0.005 0.001 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.13541 ( 1140) hydrogen bonds : angle 4.28868 ( 3384) SS BOND : bond 0.00533 ( 36) SS BOND : angle 1.28979 ( 72) covalent geometry : bond 0.00324 (16740) covalent geometry : angle 0.69017 (22452) *********************** 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 : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.8473 (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 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: 0.8612 (t) REVERT: E 63 ASN cc_start: 0.8735 (m-40) cc_final: 0.8343 (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: 0.6266 (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: 0.6204 (t80) REVERT: G 210 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6777 (mm-30) REVERT: H 210 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6841 (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: 0.8393 (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: 0.7956 (tt0) REVERT: J 93 PHE cc_start: 0.6606 (t80) cc_final: 0.6294 (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: 2.1325 time to fit residues: 694.8650 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 : 2.254 ------------------------------------------------------------------------------- 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 162 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.181114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131104 restraints weight = 41778.398| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.40 r_work: 0.3362 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1305 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= 0.153 Angle : 0.556 4.245 22524 Z= 0.304 Chirality : 0.041 0.131 2556 Planarity : 0.004 0.035 2700 Dihedral : 6.101 32.369 2679 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.91 % Allowed : 15.36 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.18), residues: 1896 helix: 3.19 (0.13), residues: 1332 sheet: 1.64 (0.41), residues: 120 loop : -1.20 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 79 HIS 0.002 0.001 HIS F 274 PHE 0.008 0.001 PHE J 53 TYR 0.013 0.002 TYR B 67 ARG 0.003 0.000 ARG G 233 Details of bonding type rmsd hydrogen bonds : bond 0.07517 ( 1140) hydrogen bonds : angle 3.39204 ( 3384) SS BOND : bond 0.00409 ( 36) SS BOND : angle 1.03491 ( 72) covalent geometry : bond 0.00314 (16740) covalent geometry : angle 0.55386 (22452) *********************** 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: 16 poor density : 234 time to evaluate : 2.389 Fit side-chains REVERT: A 210 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6817 (mm-30) REVERT: B 52 MET cc_start: 0.8749 (mmt) cc_final: 0.8348 (mmt) REVERT: B 93 PHE cc_start: 0.6405 (t80) cc_final: 0.6097 (t80) REVERT: B 210 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6847 (mm-30) REVERT: B 239 GLU cc_start: 0.8529 (tt0) cc_final: 0.8300 (tt0) REVERT: C 93 PHE cc_start: 0.6511 (t80) cc_final: 0.6221 (t80) REVERT: C 210 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6705 (mm-30) REVERT: D 210 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6820 (mm-30) REVERT: E 52 MET cc_start: 0.8977 (mmt) cc_final: 0.8114 (mmt) REVERT: E 63 ASN cc_start: 0.8687 (m-40) cc_final: 0.8481 (m110) REVERT: E 93 PHE cc_start: 0.6549 (t80) cc_final: 0.6281 (t80) REVERT: E 210 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6912 (mm-30) REVERT: E 239 GLU cc_start: 0.8497 (tt0) cc_final: 0.8269 (tt0) REVERT: F 85 MET cc_start: 0.7855 (tpt) cc_final: 0.7498 (tpt) REVERT: F 93 PHE cc_start: 0.6540 (t80) cc_final: 0.6244 (t80) REVERT: F 210 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6785 (mm-30) REVERT: G 85 MET cc_start: 0.7896 (tpt) cc_final: 0.7595 (tpt) REVERT: G 93 PHE cc_start: 0.6562 (t80) cc_final: 0.6244 (t80) REVERT: G 210 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6711 (mm-30) REVERT: G 253 PHE cc_start: 0.8298 (t80) cc_final: 0.8080 (t80) REVERT: H 210 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6846 (mm-30) REVERT: I 52 MET cc_start: 0.8792 (mmt) cc_final: 0.8422 (mmt) REVERT: I 210 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6877 (mm-30) REVERT: I 239 GLU cc_start: 0.8386 (tt0) cc_final: 0.8155 (tt0) REVERT: J 85 MET cc_start: 0.7920 (tpt) cc_final: 0.7571 (tpt) REVERT: J 93 PHE cc_start: 0.6591 (t80) cc_final: 0.6255 (t80) REVERT: J 210 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6699 (mm-30) REVERT: K 210 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6830 (mm-30) REVERT: L 93 PHE cc_start: 0.6462 (t80) cc_final: 0.6181 (t80) REVERT: L 210 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6779 (mm-30) outliers start: 16 outliers final: 9 residues processed: 235 average time/residue: 2.1812 time to fit residues: 580.7493 Evaluate side-chains 234 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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 J residue 41 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 186 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 K 207 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.175451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126651 restraints weight = 42366.089| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.40 r_work: 0.3310 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1710 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= 0.162 Angle : 0.583 4.677 22524 Z= 0.311 Chirality : 0.043 0.142 2556 Planarity : 0.004 0.042 2700 Dihedral : 6.947 34.903 2676 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.30 % Allowed : 14.97 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.18), residues: 1896 helix: 3.41 (0.13), residues: 1332 sheet: 2.09 (0.45), residues: 120 loop : -1.38 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP H 79 HIS 0.003 0.001 HIS J 75 PHE 0.010 0.001 PHE I 53 TYR 0.014 0.002 TYR G 243 ARG 0.002 0.000 ARG G 69 Details of bonding type rmsd hydrogen bonds : bond 0.07801 ( 1140) hydrogen bonds : angle 3.26736 ( 3384) SS BOND : bond 0.00543 ( 36) SS BOND : angle 1.31028 ( 72) covalent geometry : bond 0.00358 (16740) covalent geometry : angle 0.57944 (22452) *********************** 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 251 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 2.492 Fit side-chains REVERT: A 210 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6708 (mm-30) REVERT: B 52 MET cc_start: 0.8849 (mmt) cc_final: 0.8467 (mmt) REVERT: B 93 PHE cc_start: 0.6482 (t80) cc_final: 0.6162 (t80) REVERT: B 210 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6725 (mm-30) REVERT: B 239 GLU cc_start: 0.8588 (tt0) cc_final: 0.8362 (tt0) REVERT: C 210 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6673 (mm-30) REVERT: D 210 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6709 (mm-30) REVERT: E 52 MET cc_start: 0.9069 (mmt) cc_final: 0.8327 (mmt) REVERT: E 63 ASN cc_start: 0.8860 (m-40) cc_final: 0.8646 (m110) REVERT: E 93 PHE cc_start: 0.6600 (t80) cc_final: 0.6309 (t80) REVERT: E 210 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6673 (mm-30) REVERT: E 239 GLU cc_start: 0.8583 (tt0) cc_final: 0.8365 (tt0) REVERT: F 85 MET cc_start: 0.7888 (tpt) cc_final: 0.7597 (tpt) REVERT: F 93 PHE cc_start: 0.6551 (t80) cc_final: 0.6222 (t80) REVERT: F 210 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6760 (mm-30) REVERT: G 93 PHE cc_start: 0.6575 (t80) cc_final: 0.6251 (t80) REVERT: G 210 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6696 (mm-30) REVERT: H 210 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6730 (mm-30) REVERT: I 52 MET cc_start: 0.8893 (mmt) cc_final: 0.8529 (mmt) REVERT: I 93 PHE cc_start: 0.6559 (t80) cc_final: 0.6274 (t80) REVERT: I 210 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6714 (mm-30) REVERT: I 239 GLU cc_start: 0.8566 (tt0) cc_final: 0.8364 (tt0) REVERT: J 210 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6729 (mm-30) REVERT: K 210 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6705 (mm-30) REVERT: L 93 PHE cc_start: 0.6496 (t80) cc_final: 0.6199 (t80) REVERT: L 210 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6719 (mm-30) outliers start: 23 outliers final: 17 residues processed: 231 average time/residue: 2.1987 time to fit residues: 579.9995 Evaluate side-chains 240 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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 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 H residue 230 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 6 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.172699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123757 restraints weight = 42562.860| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.41 r_work: 0.3266 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16776 Z= 0.194 Angle : 0.627 5.099 22524 Z= 0.331 Chirality : 0.044 0.145 2556 Planarity : 0.005 0.049 2700 Dihedral : 8.143 38.856 2676 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.47 % Allowed : 14.23 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.18), residues: 1896 helix: 3.26 (0.12), residues: 1332 sheet: 1.92 (0.47), residues: 120 loop : -1.74 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 79 HIS 0.005 0.001 HIS J 75 PHE 0.012 0.001 PHE L 53 TYR 0.015 0.003 TYR F 243 ARG 0.003 0.001 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.08349 ( 1140) hydrogen bonds : angle 3.25899 ( 3384) SS BOND : bond 0.00714 ( 36) SS BOND : angle 1.61733 ( 72) covalent geometry : bond 0.00451 (16740) covalent geometry : angle 0.62166 (22452) *********************** 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 240 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 2.477 Fit side-chains revert: symmetry clash REVERT: A 210 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6806 (mm-30) REVERT: B 52 MET cc_start: 0.8950 (mmt) cc_final: 0.8599 (mmt) REVERT: B 93 PHE cc_start: 0.6678 (t80) cc_final: 0.6405 (t80) REVERT: B 210 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6821 (mm-30) REVERT: B 239 GLU cc_start: 0.8664 (tt0) cc_final: 0.8427 (tt0) REVERT: C 210 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6903 (mm-30) REVERT: D 210 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6811 (mm-30) REVERT: E 210 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6791 (mm-30) REVERT: E 239 GLU cc_start: 0.8659 (tt0) cc_final: 0.8455 (tt0) REVERT: F 210 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6918 (mm-30) REVERT: F 232 ASN cc_start: 0.8343 (p0) cc_final: 0.8141 (p0) REVERT: G 210 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6870 (mm-30) REVERT: H 210 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6794 (mm-30) REVERT: I 52 MET cc_start: 0.8953 (mmt) cc_final: 0.8603 (mmt) REVERT: I 210 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6832 (mm-30) REVERT: J 210 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6882 (mm-30) REVERT: K 210 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6791 (mm-30) REVERT: L 210 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6834 (mm-30) outliers start: 26 outliers final: 17 residues processed: 216 average time/residue: 2.2481 time to fit residues: 551.3035 Evaluate side-chains 218 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 2.302 ------------------------------------------------------------------------------- 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 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 H residue 230 GLU 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 230 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 116 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.173990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126433 restraints weight = 42235.343| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.44 r_work: 0.3293 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16776 Z= 0.158 Angle : 0.571 4.578 22524 Z= 0.302 Chirality : 0.042 0.135 2556 Planarity : 0.004 0.046 2700 Dihedral : 7.710 40.913 2676 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.30 % Allowed : 15.02 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.18), residues: 1896 helix: 3.45 (0.12), residues: 1332 sheet: 2.18 (0.46), residues: 120 loop : -1.66 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 79 HIS 0.003 0.001 HIS C 75 PHE 0.010 0.001 PHE L 53 TYR 0.013 0.002 TYR F 243 ARG 0.002 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.07530 ( 1140) hydrogen bonds : angle 3.22316 ( 3384) SS BOND : bond 0.00497 ( 36) SS BOND : angle 1.30067 ( 72) covalent geometry : bond 0.00354 (16740) covalent geometry : angle 0.56738 (22452) *********************** 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 223 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 2.443 Fit side-chains REVERT: A 210 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6773 (mm-30) REVERT: B 52 MET cc_start: 0.8938 (mmt) cc_final: 0.8600 (mmt) REVERT: B 210 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6801 (mm-30) REVERT: C 210 GLU cc_start: 0.7632 (mt-10) cc_final: 0.6930 (mm-30) REVERT: D 210 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6748 (mm-30) REVERT: E 210 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6792 (mm-30) REVERT: E 239 GLU cc_start: 0.8684 (tt0) cc_final: 0.8441 (tt0) REVERT: F 210 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6873 (mm-30) REVERT: G 210 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6818 (mm-30) REVERT: H 210 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6776 (mm-30) REVERT: I 52 MET cc_start: 0.8965 (mmt) cc_final: 0.8627 (mmt) REVERT: I 210 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6800 (mm-30) REVERT: J 210 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6885 (mm-30) REVERT: K 210 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6753 (mm-30) REVERT: L 210 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6774 (mm-30) outliers start: 23 outliers final: 16 residues processed: 202 average time/residue: 2.2800 time to fit residues: 520.0819 Evaluate side-chains 207 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 2.279 ------------------------------------------------------------------------------- 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 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 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 H residue 230 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 149 optimal weight: 0.0050 chunk 133 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 75 HIS F 207 ASN G 75 HIS 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.177072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129109 restraints weight = 42511.692| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.40 r_work: 0.3352 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2387 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= 0.118 Angle : 0.502 4.530 22524 Z= 0.266 Chirality : 0.040 0.124 2556 Planarity : 0.004 0.038 2700 Dihedral : 6.314 34.644 2676 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.79 % Allowed : 15.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.18), residues: 1896 helix: 3.72 (0.12), residues: 1332 sheet: 2.25 (0.43), residues: 120 loop : -1.47 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 79 HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE I 53 TYR 0.010 0.002 TYR D 67 ARG 0.002 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.06187 ( 1140) hydrogen bonds : angle 3.11973 ( 3384) SS BOND : bond 0.00253 ( 36) SS BOND : angle 0.78560 ( 72) covalent geometry : bond 0.00238 (16740) covalent geometry : angle 0.50065 (22452) *********************** 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 211 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 2.379 Fit side-chains REVERT: A 210 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6565 (mm-30) REVERT: B 52 MET cc_start: 0.8826 (mmt) cc_final: 0.8530 (mmt) REVERT: B 210 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6588 (mm-30) REVERT: B 239 GLU cc_start: 0.8580 (tt0) cc_final: 0.8298 (tt0) REVERT: C 210 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6700 (mm-30) REVERT: D 210 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6542 (mm-30) REVERT: E 210 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6546 (mm-30) REVERT: E 239 GLU cc_start: 0.8581 (tt0) cc_final: 0.8299 (tt0) REVERT: F 210 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6675 (mm-30) REVERT: G 43 GLU cc_start: 0.7542 (tt0) cc_final: 0.7256 (tt0) REVERT: G 210 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6669 (mm-30) REVERT: H 210 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6553 (mm-30) REVERT: I 52 MET cc_start: 0.8852 (mmt) cc_final: 0.8556 (mmt) REVERT: I 210 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6594 (mm-30) REVERT: J 210 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6661 (mm-30) REVERT: K 210 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6545 (mm-30) REVERT: L 210 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6566 (mm-30) outliers start: 14 outliers final: 11 residues processed: 198 average time/residue: 2.2504 time to fit residues: 505.0407 Evaluate side-chains 198 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 106 optimal weight: 0.0000 chunk 137 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.175996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126779 restraints weight = 42377.369| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.44 r_work: 0.3294 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2483 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= 0.139 Angle : 0.542 4.518 22524 Z= 0.284 Chirality : 0.042 0.139 2556 Planarity : 0.004 0.041 2700 Dihedral : 6.782 34.489 2676 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.08 % Allowed : 16.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.18), residues: 1896 helix: 3.73 (0.12), residues: 1332 sheet: 2.15 (0.44), residues: 120 loop : -1.49 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 79 HIS 0.004 0.001 HIS G 75 PHE 0.010 0.001 PHE L 53 TYR 0.013 0.002 TYR F 243 ARG 0.002 0.000 ARG G 69 Details of bonding type rmsd hydrogen bonds : bond 0.06597 ( 1140) hydrogen bonds : angle 3.06372 ( 3384) SS BOND : bond 0.00443 ( 36) SS BOND : angle 1.14605 ( 72) covalent geometry : bond 0.00304 (16740) covalent geometry : angle 0.53880 (22452) *********************** 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 210 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 2.663 Fit side-chains REVERT: A 210 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6657 (mm-30) REVERT: B 52 MET cc_start: 0.8907 (mmt) cc_final: 0.8544 (mmt) REVERT: B 210 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6742 (mm-30) REVERT: C 210 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6832 (mm-30) REVERT: D 210 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6635 (mm-30) REVERT: E 210 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6725 (mm-30) REVERT: F 210 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6822 (mm-30) REVERT: G 210 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6822 (mm-30) REVERT: H 210 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6637 (mm-30) REVERT: I 52 MET cc_start: 0.8922 (mmt) cc_final: 0.8552 (mmt) REVERT: I 210 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6730 (mm-30) REVERT: J 210 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6817 (mm-30) REVERT: K 210 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6641 (mm-30) REVERT: L 210 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6727 (mm-30) outliers start: 19 outliers final: 15 residues processed: 191 average time/residue: 2.3092 time to fit residues: 499.2344 Evaluate side-chains 198 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 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 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 J residue 41 VAL Chi-restraints excluded: chain K 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 53 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.175099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127449 restraints weight = 42349.462| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.37 r_work: 0.3290 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16776 Z= 0.155 Angle : 0.566 4.630 22524 Z= 0.297 Chirality : 0.043 0.142 2556 Planarity : 0.004 0.043 2700 Dihedral : 7.199 34.650 2676 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.36 % Allowed : 15.82 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.79 (0.18), residues: 1896 helix: 3.69 (0.12), residues: 1332 sheet: 2.34 (0.47), residues: 120 loop : -1.52 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 79 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE K 53 TYR 0.013 0.002 TYR J 243 ARG 0.002 0.000 ARG H 233 Details of bonding type rmsd hydrogen bonds : bond 0.06995 ( 1140) hydrogen bonds : angle 3.06981 ( 3384) SS BOND : bond 0.00539 ( 36) SS BOND : angle 1.28871 ( 72) covalent geometry : bond 0.00352 (16740) covalent geometry : angle 0.56234 (22452) *********************** 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 220 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 2.294 Fit side-chains REVERT: A 210 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6585 (mm-30) REVERT: B 52 MET cc_start: 0.8916 (mmt) cc_final: 0.8541 (mmt) REVERT: B 210 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6616 (mm-30) REVERT: C 210 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6748 (mm-30) REVERT: D 85 MET cc_start: 0.7882 (tpt) cc_final: 0.7196 (tpt) REVERT: D 210 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6562 (mm-30) REVERT: E 210 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6591 (mm-30) REVERT: F 210 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6720 (mm-30) REVERT: G 210 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6725 (mm-30) REVERT: H 210 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6555 (mm-30) REVERT: I 52 MET cc_start: 0.8920 (mmt) cc_final: 0.8544 (mmt) REVERT: I 210 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6599 (mm-30) REVERT: J 210 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6724 (mm-30) REVERT: K 85 MET cc_start: 0.7891 (tpt) cc_final: 0.7259 (tpt) REVERT: K 210 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6538 (mm-30) REVERT: L 210 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6593 (mm-30) outliers start: 24 outliers final: 19 residues processed: 202 average time/residue: 2.2211 time to fit residues: 507.5207 Evaluate side-chains 207 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 230 GLU 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 F residue 230 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 83 ILE 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 83 ILE Chi-restraints excluded: chain L residue 230 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 186 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.176642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130326 restraints weight = 41744.257| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.17 r_work: 0.3357 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2610 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= 0.132 Angle : 0.529 4.486 22524 Z= 0.279 Chirality : 0.041 0.134 2556 Planarity : 0.004 0.039 2700 Dihedral : 6.697 34.479 2676 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.96 % Allowed : 16.38 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.18), residues: 1896 helix: 3.77 (0.12), residues: 1332 sheet: 2.45 (0.47), residues: 120 loop : -1.44 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 79 HIS 0.002 0.000 HIS E 75 PHE 0.009 0.001 PHE L 53 TYR 0.012 0.002 TYR F 243 ARG 0.001 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.06421 ( 1140) hydrogen bonds : angle 3.04472 ( 3384) SS BOND : bond 0.00395 ( 36) SS BOND : angle 1.04646 ( 72) covalent geometry : bond 0.00283 (16740) covalent geometry : angle 0.52641 (22452) *********************** 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 209 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 2.285 Fit side-chains REVERT: A 210 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6634 (mm-30) REVERT: B 52 MET cc_start: 0.8861 (mmt) cc_final: 0.8453 (mmt) REVERT: B 210 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6686 (mm-30) REVERT: C 210 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6766 (mm-30) REVERT: D 85 MET cc_start: 0.7835 (tpt) cc_final: 0.7129 (tpt) REVERT: D 210 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6577 (mm-30) REVERT: E 210 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6675 (mm-30) REVERT: F 210 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6762 (mm-30) REVERT: G 210 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6767 (mm-30) REVERT: H 85 MET cc_start: 0.7859 (tpt) cc_final: 0.7162 (tpt) REVERT: H 210 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6613 (mm-30) REVERT: I 52 MET cc_start: 0.8877 (mmt) cc_final: 0.8473 (mmt) REVERT: I 210 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6688 (mm-30) REVERT: J 210 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6737 (mm-30) REVERT: K 85 MET cc_start: 0.7838 (tpt) cc_final: 0.7177 (tpt) REVERT: K 210 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6593 (mm-30) REVERT: L 210 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6692 (mm-30) outliers start: 17 outliers final: 14 residues processed: 197 average time/residue: 2.2234 time to fit residues: 496.6713 Evaluate side-chains 204 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 83 ILE 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 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 K residue 83 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 173 optimal weight: 0.0770 chunk 185 optimal weight: 4.9990 overall best weight: 1.7942 ------------------------------------------------------------------------------- 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 207 ASN G 207 ASN H 207 ASN K 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129304 restraints weight = 41574.826| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.17 r_work: 0.3345 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2684 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= 0.146 Angle : 0.554 5.118 22524 Z= 0.291 Chirality : 0.042 0.140 2556 Planarity : 0.004 0.043 2700 Dihedral : 6.959 34.408 2676 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.85 % Allowed : 16.78 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.18), residues: 1896 helix: 3.76 (0.12), residues: 1332 sheet: 2.51 (0.48), residues: 120 loop : -1.46 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 79 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE J 205 TYR 0.012 0.002 TYR J 243 ARG 0.002 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.06695 ( 1140) hydrogen bonds : angle 3.03790 ( 3384) SS BOND : bond 0.00474 ( 36) SS BOND : angle 1.20590 ( 72) covalent geometry : bond 0.00325 (16740) covalent geometry : angle 0.55064 (22452) ********************** 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 211 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 2.468 Fit side-chains REVERT: A 210 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6697 (mm-30) REVERT: B 52 MET cc_start: 0.8889 (mmt) cc_final: 0.8486 (mmt) REVERT: B 210 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6684 (mm-30) REVERT: C 210 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6809 (mm-30) REVERT: D 85 MET cc_start: 0.7895 (tpt) cc_final: 0.7172 (tpt) REVERT: D 210 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6619 (mm-30) REVERT: E 210 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6688 (mm-30) REVERT: F 210 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6788 (mm-30) REVERT: G 210 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6799 (mm-30) REVERT: H 85 MET cc_start: 0.7910 (tpt) cc_final: 0.7251 (tpt) REVERT: H 210 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6637 (mm-30) REVERT: I 52 MET cc_start: 0.8899 (mmt) cc_final: 0.8498 (mmt) REVERT: I 210 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6688 (mm-30) REVERT: J 210 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6757 (mm-30) REVERT: K 85 MET cc_start: 0.7892 (tpt) cc_final: 0.7220 (tpt) REVERT: K 210 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6644 (mm-30) REVERT: L 210 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6704 (mm-30) outliers start: 15 outliers final: 15 residues processed: 199 average time/residue: 2.2804 time to fit residues: 515.8308 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 : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 83 ILE 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 F residue 230 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 83 ILE 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 83 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 32 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 207 ASN H 207 ASN J 207 ASN K 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128454 restraints weight = 41436.065| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.21 r_work: 0.3322 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16776 Z= 0.162 Angle : 0.581 4.793 22524 Z= 0.306 Chirality : 0.043 0.143 2556 Planarity : 0.004 0.045 2700 Dihedral : 7.507 36.719 2676 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.19 % Allowed : 16.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.18), residues: 1896 helix: 3.69 (0.12), residues: 1332 sheet: 2.59 (0.50), residues: 120 loop : -1.49 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 79 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE L 53 TYR 0.013 0.002 TYR F 243 ARG 0.002 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.07122 ( 1140) hydrogen bonds : angle 3.06436 ( 3384) SS BOND : bond 0.00562 ( 36) SS BOND : angle 1.36308 ( 72) covalent geometry : bond 0.00370 (16740) covalent geometry : angle 0.57705 (22452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19211.33 seconds wall clock time: 328 minutes 53.81 seconds (19733.81 seconds total)