Starting phenix.real_space_refine on Sat Jun 28 04:32:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xh8_38344/06_2025/8xh8_38344_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xh8_38344/06_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_38344/06_2025/8xh8_38344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xh8_38344/06_2025/8xh8_38344.map" model { file = "/net/cci-nas-00/data/ceres_data/8xh8_38344/06_2025/8xh8_38344_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xh8_38344/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.25, per 1000 atoms: 0.51 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: 8.33 Conformation dependent library (CDL) restraints added in 2.4 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: 2.49 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: 10.72 Time building geometry restraints manager: 10.21 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.640 Extract box with map and model: 1.340 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 64.590 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.630 ------------------------------------------------------------------------------- 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 : 2.378 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: 2.1184 time to fit residues: 691.9601 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 : 2.225 ------------------------------------------------------------------------------- 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 = 0.131103 restraints weight = 41778.186| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.40 r_work: 0.3362 rms_B_bonded: 1.95 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: 0.8321 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 32.368 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 3.39207 ( 3384) SS BOND : bond 0.00408 ( 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 : 2.291 Fit side-chains REVERT: A 210 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6804 (mm-30) REVERT: B 52 MET cc_start: 0.8750 (mmt) cc_final: 0.8349 (mmt) REVERT: B 93 PHE cc_start: 0.6392 (t80) cc_final: 0.6084 (t80) REVERT: B 210 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6835 (mm-30) REVERT: B 239 GLU cc_start: 0.8531 (tt0) cc_final: 0.8302 (tt0) REVERT: C 93 PHE cc_start: 0.6498 (t80) cc_final: 0.6207 (t80) REVERT: C 210 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6694 (mm-30) REVERT: D 210 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6809 (mm-30) REVERT: E 52 MET cc_start: 0.8976 (mmt) cc_final: 0.8111 (mmt) REVERT: E 63 ASN cc_start: 0.8687 (m-40) cc_final: 0.8482 (m110) REVERT: E 93 PHE cc_start: 0.6537 (t80) cc_final: 0.6267 (t80) REVERT: E 210 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6902 (mm-30) REVERT: E 239 GLU cc_start: 0.8495 (tt0) cc_final: 0.8266 (tt0) REVERT: F 85 MET cc_start: 0.7853 (tpt) cc_final: 0.7495 (tpt) REVERT: F 93 PHE cc_start: 0.6526 (t80) cc_final: 0.6230 (t80) REVERT: F 210 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6777 (mm-30) REVERT: G 85 MET cc_start: 0.7890 (tpt) cc_final: 0.7589 (tpt) REVERT: G 93 PHE cc_start: 0.6548 (t80) cc_final: 0.6230 (t80) REVERT: G 210 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6701 (mm-30) REVERT: G 253 PHE cc_start: 0.8297 (t80) cc_final: 0.8079 (t80) REVERT: H 210 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6833 (mm-30) REVERT: I 52 MET cc_start: 0.8793 (mmt) cc_final: 0.8424 (mmt) REVERT: I 210 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6863 (mm-30) REVERT: I 239 GLU cc_start: 0.8390 (tt0) cc_final: 0.8158 (tt0) REVERT: J 85 MET cc_start: 0.7918 (tpt) cc_final: 0.7571 (tpt) REVERT: J 93 PHE cc_start: 0.6578 (t80) cc_final: 0.6241 (t80) REVERT: J 210 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6688 (mm-30) REVERT: K 210 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6820 (mm-30) REVERT: L 93 PHE cc_start: 0.6447 (t80) cc_final: 0.6167 (t80) REVERT: L 210 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6769 (mm-30) outliers start: 16 outliers final: 9 residues processed: 235 average time/residue: 2.2135 time to fit residues: 590.6741 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 : 2.373 ------------------------------------------------------------------------------- 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: 4.9990 chunk 72 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- 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 G 268 ASN H 207 ASN I 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 = 0.3959 r_free = 0.3959 target = 0.176273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128911 restraints weight = 42365.555| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.39 r_work: 0.3319 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16776 Z= 0.153 Angle : 0.562 4.537 22524 Z= 0.300 Chirality : 0.042 0.141 2556 Planarity : 0.004 0.040 2700 Dihedral : 6.642 35.075 2676 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 3.57 (0.18), residues: 1896 helix: 3.46 (0.12), residues: 1332 sheet: 2.12 (0.44), residues: 120 loop : -1.33 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 79 HIS 0.004 0.001 HIS J 75 PHE 0.009 0.001 PHE I 53 TYR 0.013 0.002 TYR G 243 ARG 0.002 0.000 ARG G 69 Details of bonding type rmsd hydrogen bonds : bond 0.07464 ( 1140) hydrogen bonds : angle 3.23257 ( 3384) SS BOND : bond 0.00474 ( 36) SS BOND : angle 1.21353 ( 72) covalent geometry : bond 0.00327 (16740) covalent geometry : angle 0.55868 (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 257 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 2.526 Fit side-chains REVERT: A 210 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6801 (mm-30) REVERT: B 52 MET cc_start: 0.8851 (mmt) cc_final: 0.8481 (mmt) REVERT: B 93 PHE cc_start: 0.6521 (t80) cc_final: 0.6198 (t80) REVERT: B 210 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6776 (mm-30) REVERT: B 239 GLU cc_start: 0.8605 (tt0) cc_final: 0.8386 (tt0) REVERT: C 210 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6763 (mm-30) REVERT: D 210 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6801 (mm-30) REVERT: E 52 MET cc_start: 0.9062 (mmt) cc_final: 0.8328 (mmt) REVERT: E 63 ASN cc_start: 0.8852 (m-40) cc_final: 0.8638 (m110) REVERT: E 93 PHE cc_start: 0.6639 (t80) cc_final: 0.6344 (t80) REVERT: E 210 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6805 (mm-30) REVERT: E 239 GLU cc_start: 0.8594 (tt0) cc_final: 0.8383 (tt0) REVERT: F 85 MET cc_start: 0.7947 (tpt) cc_final: 0.7651 (tpt) REVERT: F 93 PHE cc_start: 0.6591 (t80) cc_final: 0.6257 (t80) REVERT: F 210 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6869 (mm-30) REVERT: G 93 PHE cc_start: 0.6612 (t80) cc_final: 0.6283 (t80) REVERT: G 210 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6759 (mm-30) REVERT: G 232 ASN cc_start: 0.8246 (p0) cc_final: 0.8041 (p0) REVERT: H 210 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6819 (mm-30) REVERT: I 52 MET cc_start: 0.8888 (mmt) cc_final: 0.8538 (mmt) REVERT: I 93 PHE cc_start: 0.6599 (t80) cc_final: 0.6312 (t80) REVERT: I 210 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6820 (mm-30) REVERT: J 210 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6814 (mm-30) REVERT: K 210 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6790 (mm-30) REVERT: L 93 PHE cc_start: 0.6535 (t80) cc_final: 0.6240 (t80) REVERT: L 210 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6818 (mm-30) outliers start: 23 outliers final: 17 residues processed: 237 average time/residue: 2.2758 time to fit residues: 621.5115 Evaluate side-chains 243 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 2.370 ------------------------------------------------------------------------------- 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: 4.9990 chunk 40 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.172886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123837 restraints weight = 42601.725| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.41 r_work: 0.3269 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16776 Z= 0.200 Angle : 0.627 5.178 22524 Z= 0.332 Chirality : 0.045 0.149 2556 Planarity : 0.005 0.046 2700 Dihedral : 7.937 35.672 2676 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.47 % Allowed : 15.08 % Favored : 83.45 % 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: 3.30 (0.18), residues: 1896 helix: 3.32 (0.12), residues: 1332 sheet: 1.95 (0.46), residues: 120 loop : -1.65 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 79 HIS 0.004 0.001 HIS G 75 PHE 0.012 0.002 PHE I 53 TYR 0.015 0.003 TYR G 243 ARG 0.002 0.000 ARG C 233 Details of bonding type rmsd hydrogen bonds : bond 0.08319 ( 1140) hydrogen bonds : angle 3.23659 ( 3384) SS BOND : bond 0.00757 ( 36) SS BOND : angle 1.66486 ( 72) covalent geometry : bond 0.00469 (16740) covalent geometry : angle 0.62107 (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 231 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 2.262 Fit side-chains REVERT: A 210 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6688 (mm-30) REVERT: B 52 MET cc_start: 0.8924 (mmt) cc_final: 0.8588 (mmt) REVERT: B 93 PHE cc_start: 0.6538 (t80) cc_final: 0.6256 (t80) REVERT: B 210 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6723 (mm-30) REVERT: C 210 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6758 (mm-30) REVERT: D 210 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6679 (mm-30) REVERT: E 210 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6747 (mm-30) REVERT: E 239 GLU cc_start: 0.8624 (tt0) cc_final: 0.8404 (tt0) REVERT: F 210 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6803 (mm-30) REVERT: G 210 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6759 (mm-30) REVERT: G 232 ASN cc_start: 0.8344 (p0) cc_final: 0.8120 (p0) REVERT: H 210 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6687 (mm-30) REVERT: I 52 MET cc_start: 0.8959 (mmt) cc_final: 0.8559 (mmt) REVERT: I 210 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6749 (mm-30) REVERT: J 210 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6775 (mm-30) REVERT: K 210 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6668 (mm-30) REVERT: L 210 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6750 (mm-30) outliers start: 26 outliers final: 17 residues processed: 206 average time/residue: 2.2547 time to fit residues: 525.7448 Evaluate side-chains 216 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 2.470 ------------------------------------------------------------------------------- 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: 0.8980 chunk 97 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.174509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127524 restraints weight = 42226.536| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.38 r_work: 0.3292 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16776 Z= 0.155 Angle : 0.564 4.520 22524 Z= 0.299 Chirality : 0.042 0.132 2556 Planarity : 0.004 0.045 2700 Dihedral : 7.397 35.162 2676 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.42 % Allowed : 15.14 % Favored : 83.45 % 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: 3.48 (0.18), residues: 1896 helix: 3.46 (0.12), residues: 1332 sheet: 2.17 (0.45), residues: 120 loop : -1.63 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.003 0.001 HIS G 75 PHE 0.010 0.001 PHE L 53 TYR 0.012 0.002 TYR L 67 ARG 0.002 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.07443 ( 1140) hydrogen bonds : angle 3.20874 ( 3384) SS BOND : bond 0.00493 ( 36) SS BOND : angle 1.26109 ( 72) covalent geometry : bond 0.00343 (16740) covalent geometry : angle 0.56050 (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 224 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 2.564 Fit side-chains REVERT: A 210 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6597 (mm-30) REVERT: B 52 MET cc_start: 0.8878 (mmt) cc_final: 0.8564 (mmt) REVERT: B 210 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6635 (mm-30) REVERT: C 210 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6673 (mm-30) REVERT: D 210 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6586 (mm-30) REVERT: E 210 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6628 (mm-30) REVERT: E 239 GLU cc_start: 0.8615 (tt0) cc_final: 0.8359 (tt0) REVERT: F 210 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6705 (mm-30) REVERT: G 210 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6665 (mm-30) REVERT: G 232 ASN cc_start: 0.8259 (p0) cc_final: 0.8024 (p0) REVERT: H 210 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6590 (mm-30) REVERT: I 52 MET cc_start: 0.8892 (mmt) cc_final: 0.8571 (mmt) REVERT: I 210 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6642 (mm-30) REVERT: J 210 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6719 (mm-30) REVERT: K 210 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6582 (mm-30) REVERT: L 210 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6609 (mm-30) outliers start: 25 outliers final: 16 residues processed: 202 average time/residue: 2.3367 time to fit residues: 533.3564 Evaluate side-chains 211 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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: 0.5980 chunk 20 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN C 75 HIS C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 75 HIS G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.175483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127094 restraints weight = 42458.949| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.40 r_work: 0.3313 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16776 Z= 0.138 Angle : 0.535 4.555 22524 Z= 0.282 Chirality : 0.041 0.133 2556 Planarity : 0.004 0.042 2700 Dihedral : 6.736 34.745 2676 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.19 % Allowed : 15.48 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.18), residues: 1896 helix: 3.62 (0.12), residues: 1332 sheet: 2.16 (0.45), residues: 120 loop : -1.53 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 79 HIS 0.003 0.001 HIS C 75 PHE 0.009 0.001 PHE H 53 TYR 0.012 0.002 TYR F 243 ARG 0.002 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.06739 ( 1140) hydrogen bonds : angle 3.11883 ( 3384) SS BOND : bond 0.00403 ( 36) SS BOND : angle 1.05306 ( 72) covalent geometry : bond 0.00296 (16740) covalent geometry : angle 0.53262 (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 219 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 2.887 Fit side-chains REVERT: A 210 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6574 (mm-30) REVERT: B 52 MET cc_start: 0.8868 (mmt) cc_final: 0.8514 (mmt) REVERT: B 210 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6617 (mm-30) REVERT: B 239 GLU cc_start: 0.8589 (tt0) cc_final: 0.8309 (tt0) REVERT: C 210 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6720 (mm-30) REVERT: D 210 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6553 (mm-30) REVERT: E 210 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6562 (mm-30) REVERT: E 239 GLU cc_start: 0.8597 (tt0) cc_final: 0.8316 (tt0) REVERT: F 210 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6701 (mm-30) REVERT: G 43 GLU cc_start: 0.7595 (tt0) cc_final: 0.7322 (tt0) REVERT: G 210 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6713 (mm-30) REVERT: G 232 ASN cc_start: 0.8304 (p0) cc_final: 0.8065 (p0) REVERT: H 210 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6578 (mm-30) REVERT: I 52 MET cc_start: 0.8891 (mmt) cc_final: 0.8535 (mmt) REVERT: I 210 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6624 (mm-30) REVERT: J 210 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6694 (mm-30) REVERT: K 210 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6574 (mm-30) REVERT: L 210 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6609 (mm-30) outliers start: 21 outliers final: 15 residues processed: 199 average time/residue: 2.3761 time to fit residues: 541.0123 Evaluate side-chains 206 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 2.475 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.173823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124240 restraints weight = 42333.505| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.42 r_work: 0.3249 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16776 Z= 0.180 Angle : 0.609 5.116 22524 Z= 0.319 Chirality : 0.044 0.147 2556 Planarity : 0.005 0.047 2700 Dihedral : 7.932 40.908 2676 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.36 % Allowed : 15.53 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.18), residues: 1896 helix: 3.52 (0.12), residues: 1332 sheet: 2.26 (0.47), residues: 120 loop : -1.65 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP D 79 HIS 0.005 0.001 HIS G 75 PHE 0.012 0.001 PHE K 53 TYR 0.014 0.002 TYR F 243 ARG 0.002 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.07684 ( 1140) hydrogen bonds : angle 3.13246 ( 3384) SS BOND : bond 0.00668 ( 36) SS BOND : angle 1.52368 ( 72) covalent geometry : bond 0.00420 (16740) covalent geometry : angle 0.60343 (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 224 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 3.439 Fit side-chains REVERT: A 210 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6572 (mm-30) REVERT: B 52 MET cc_start: 0.8957 (mmt) cc_final: 0.8603 (mmt) REVERT: B 210 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6604 (mm-30) REVERT: C 210 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6734 (mm-30) REVERT: D 210 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6532 (mm-30) REVERT: E 210 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6571 (mm-30) REVERT: E 239 GLU cc_start: 0.8623 (tt0) cc_final: 0.8419 (tt0) REVERT: F 210 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6735 (mm-30) REVERT: G 210 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6685 (mm-30) REVERT: G 232 ASN cc_start: 0.8297 (p0) cc_final: 0.8060 (p0) REVERT: H 210 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6535 (mm-30) REVERT: I 52 MET cc_start: 0.8984 (mmt) cc_final: 0.8643 (mmt) REVERT: I 210 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6595 (mm-30) REVERT: J 210 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6694 (mm-30) REVERT: K 210 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6529 (mm-30) REVERT: L 210 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6606 (mm-30) outliers start: 24 outliers final: 19 residues processed: 203 average time/residue: 2.7597 time to fit residues: 637.9395 Evaluate side-chains 213 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 4.644 ------------------------------------------------------------------------------- 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 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 83 ILE Chi-restraints excluded: chain K residue 230 GLU 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: 2.9990 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: 0.9980 chunk 136 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.174503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125964 restraints weight = 42255.635| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.46 r_work: 0.3256 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16776 Z= 0.159 Angle : 0.578 4.664 22524 Z= 0.303 Chirality : 0.043 0.139 2556 Planarity : 0.004 0.047 2700 Dihedral : 7.770 44.648 2676 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.42 % Allowed : 15.87 % Favored : 82.71 % 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: 3.64 (0.18), residues: 1896 helix: 3.58 (0.12), residues: 1332 sheet: 2.30 (0.47), residues: 120 loop : -1.58 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.003 0.001 HIS F 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 0.07305 ( 1140) hydrogen bonds : angle 3.12399 ( 3384) SS BOND : bond 0.00540 ( 36) SS BOND : angle 1.33866 ( 72) covalent geometry : bond 0.00360 (16740) covalent geometry : angle 0.57344 (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 224 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 2.298 Fit side-chains REVERT: A 210 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6776 (mm-30) REVERT: B 52 MET cc_start: 0.8991 (mmt) cc_final: 0.8610 (mmt) REVERT: B 210 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6835 (mm-30) REVERT: C 210 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6942 (mm-30) REVERT: D 210 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6730 (mm-30) REVERT: E 210 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6805 (mm-30) REVERT: F 210 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6925 (mm-30) REVERT: G 210 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6945 (mm-30) REVERT: G 232 ASN cc_start: 0.8276 (p0) cc_final: 0.8052 (p0) REVERT: H 210 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6749 (mm-30) REVERT: I 52 MET cc_start: 0.8991 (mmt) cc_final: 0.8601 (mmt) REVERT: I 210 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6787 (mm-30) REVERT: J 210 GLU cc_start: 0.7623 (mt-10) cc_final: 0.6904 (mm-30) REVERT: K 210 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6740 (mm-30) REVERT: L 210 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6803 (mm-30) outliers start: 25 outliers final: 18 residues processed: 204 average time/residue: 2.5360 time to fit residues: 588.3233 Evaluate side-chains 211 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 2.672 ------------------------------------------------------------------------------- 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 83 ILE 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 83 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 186 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 75 HIS C 207 ASN D 207 ASN E 75 HIS E 207 ASN F 75 HIS F 207 ASN G 207 ASN H 207 ASN I 75 HIS I 207 ASN J 75 HIS J 207 ASN K 75 HIS K 207 ASN L 75 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.180310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134823 restraints weight = 41649.844| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.17 r_work: 0.3386 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16776 Z= 0.109 Angle : 0.482 6.786 22524 Z= 0.255 Chirality : 0.040 0.123 2556 Planarity : 0.003 0.034 2700 Dihedral : 5.947 34.261 2676 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.62 % Allowed : 17.12 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.19), residues: 1896 helix: 3.93 (0.12), residues: 1332 sheet: 2.62 (0.44), residues: 120 loop : -1.36 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 79 HIS 0.002 0.001 HIS G 274 PHE 0.010 0.001 PHE G 205 TYR 0.010 0.001 TYR G 243 ARG 0.001 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 1140) hydrogen bonds : angle 3.01889 ( 3384) SS BOND : bond 0.00143 ( 36) SS BOND : angle 0.73191 ( 72) covalent geometry : bond 0.00218 (16740) covalent geometry : angle 0.48108 (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 205 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 2.231 Fit side-chains REVERT: A 210 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6618 (mm-30) REVERT: B 52 MET cc_start: 0.8797 (mmt) cc_final: 0.8450 (mmt) REVERT: B 210 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6681 (mm-30) REVERT: B 239 GLU cc_start: 0.8614 (tt0) cc_final: 0.8410 (tt0) REVERT: C 210 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6741 (mm-30) REVERT: D 210 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6579 (mm-30) REVERT: E 210 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6664 (mm-30) REVERT: F 210 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6726 (mm-30) REVERT: G 210 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6754 (mm-30) REVERT: H 85 MET cc_start: 0.7810 (tpt) cc_final: 0.7142 (tpt) REVERT: H 210 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6609 (mm-30) REVERT: I 52 MET cc_start: 0.8843 (mmt) cc_final: 0.8494 (mmt) REVERT: I 210 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6671 (mm-30) REVERT: J 210 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6729 (mm-30) REVERT: K 85 MET cc_start: 0.7793 (tpt) cc_final: 0.7116 (tpt) REVERT: K 210 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6602 (mm-30) REVERT: L 210 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6668 (mm-30) outliers start: 11 outliers final: 11 residues processed: 194 average time/residue: 2.3298 time to fit residues: 510.2306 Evaluate side-chains 200 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 1.9990 chunk 187 optimal weight: 0.0980 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: 1.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.178694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132871 restraints weight = 41464.425| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.16 r_work: 0.3374 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2675 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= 0.122 Angle : 0.516 5.287 22524 Z= 0.269 Chirality : 0.041 0.137 2556 Planarity : 0.003 0.035 2700 Dihedral : 6.214 33.847 2676 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.68 % Allowed : 17.63 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.18 (0.18), residues: 1896 helix: 3.95 (0.12), residues: 1332 sheet: 2.54 (0.45), residues: 120 loop : -1.30 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 79 HIS 0.003 0.001 HIS L 75 PHE 0.008 0.001 PHE B 53 TYR 0.011 0.002 TYR F 243 ARG 0.001 0.000 ARG G 69 Details of bonding type rmsd hydrogen bonds : bond 0.05878 ( 1140) hydrogen bonds : angle 2.98220 ( 3384) SS BOND : bond 0.00304 ( 36) SS BOND : angle 0.97985 ( 72) covalent geometry : bond 0.00260 (16740) covalent geometry : angle 0.51356 (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 207 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 2.278 Fit side-chains REVERT: A 85 MET cc_start: 0.7828 (tpt) cc_final: 0.7173 (tpt) REVERT: A 210 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6626 (mm-30) REVERT: B 52 MET cc_start: 0.8850 (mmt) cc_final: 0.8449 (mmt) REVERT: B 210 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6659 (mm-30) REVERT: B 239 GLU cc_start: 0.8612 (tt0) cc_final: 0.8409 (tt0) REVERT: C 210 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6756 (mm-30) REVERT: D 85 MET cc_start: 0.7821 (tpt) cc_final: 0.7118 (tpt) REVERT: D 210 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6578 (mm-30) REVERT: E 210 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6654 (mm-30) REVERT: F 210 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6752 (mm-30) REVERT: G 210 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6790 (mm-30) REVERT: H 85 MET cc_start: 0.7844 (tpt) cc_final: 0.7199 (tpt) REVERT: H 210 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6617 (mm-30) REVERT: I 52 MET cc_start: 0.8890 (mmt) cc_final: 0.8488 (mmt) REVERT: I 210 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6664 (mm-30) REVERT: J 210 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6772 (mm-30) REVERT: K 85 MET cc_start: 0.7834 (tpt) cc_final: 0.7187 (tpt) REVERT: K 210 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6608 (mm-30) REVERT: L 210 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6661 (mm-30) outliers start: 12 outliers final: 11 residues processed: 196 average time/residue: 2.2836 time to fit residues: 508.6197 Evaluate side-chains 205 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 32 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN D 207 ASN F 207 ASN G 207 ASN H 207 ASN 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 = 0.3961 r_free = 0.3961 target = 0.177316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130957 restraints weight = 41429.195| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.43 r_work: 0.3335 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2735 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= 0.138 Angle : 0.544 5.153 22524 Z= 0.284 Chirality : 0.042 0.140 2556 Planarity : 0.004 0.040 2700 Dihedral : 6.664 34.038 2676 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.68 % Allowed : 17.74 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.18), residues: 1896 helix: 3.87 (0.12), residues: 1332 sheet: 2.53 (0.47), residues: 120 loop : -1.38 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 79 HIS 0.003 0.001 HIS C 75 PHE 0.009 0.001 PHE I 53 TYR 0.013 0.002 TYR A 243 ARG 0.001 0.000 ARG K 206 Details of bonding type rmsd hydrogen bonds : bond 0.06366 ( 1140) hydrogen bonds : angle 2.99422 ( 3384) SS BOND : bond 0.00435 ( 36) SS BOND : angle 1.14522 ( 72) covalent geometry : bond 0.00306 (16740) covalent geometry : angle 0.54071 (22452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20077.81 seconds wall clock time: 345 minutes 42.75 seconds (20742.75 seconds total)