Starting phenix.real_space_refine on Thu Feb 5 17:37:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xl8_33274/02_2026/7xl8_33274_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xl8_33274/02_2026/7xl8_33274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xl8_33274/02_2026/7xl8_33274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xl8_33274/02_2026/7xl8_33274.map" model { file = "/net/cci-nas-00/data/ceres_data/7xl8_33274/02_2026/7xl8_33274_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xl8_33274/02_2026/7xl8_33274_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 11556 2.51 5 N 2508 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16920 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "B" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "C" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "D" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "E" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "F" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "G" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "I" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "J" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "K" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "L" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "J" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "K" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Chain: "L" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 3.48, per 1000 atoms: 0.21 Number of scatterers: 16920 At special positions: 0 Unit cell: (93.4065, 100.139, 143.897, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 2700 8.00 N 2508 7.00 C 11556 6.00 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=2.05 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.05 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.05 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.05 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.05 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.05 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.05 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.05 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.05 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.05 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.05 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.05 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.05 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.05 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.05 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.05 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.05 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.05 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.05 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.05 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.05 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.05 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.05 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.05 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.05 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=2.05 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.05 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.05 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.05 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.05 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.04 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.05 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: 1.19 Conformation dependent library (CDL) restraints added in 702.9 milliseconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 73.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 22 through 41 removed outlier: 3.593A pdb=" N VAL A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.744A 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 removed outlier: 3.577A pdb=" N TYR A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.504A pdb=" N SER A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 276 removed outlier: 3.624A pdb=" N GLU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 41 removed outlier: 3.594A pdb=" N VAL B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.744A 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 removed outlier: 3.577A pdb=" N TYR B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.504A pdb=" N SER B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 276 removed outlier: 3.625A pdb=" N GLU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 41 removed outlier: 3.593A pdb=" N VAL C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.744A 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 removed outlier: 3.578A pdb=" N TYR C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.504A pdb=" N SER C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 276 removed outlier: 3.624A pdb=" N GLU C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 41 removed outlier: 3.594A pdb=" N VAL D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 39 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.744A 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 removed outlier: 3.577A pdb=" N TYR D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.504A pdb=" N SER D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 276 removed outlier: 3.624A pdb=" N GLU D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 41 removed outlier: 3.593A pdb=" N VAL E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.744A 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 removed outlier: 3.578A pdb=" N TYR E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 removed outlier: 3.504A pdb=" N SER E 97 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE E 201 " --> pdb=" O ARG E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 276 removed outlier: 3.625A pdb=" N GLU E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 41 removed outlier: 3.594A pdb=" N VAL F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 39 " --> pdb=" O ILE F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.743A 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 removed outlier: 3.578A pdb=" N TYR F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 100 removed outlier: 3.504A pdb=" N SER F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 221 removed outlier: 3.682A pdb=" N ILE F 201 " --> pdb=" O ARG F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 276 removed outlier: 3.624A pdb=" N GLU F 271 " --> pdb=" O LEU F 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 41 removed outlier: 3.593A pdb=" N VAL G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 39 " --> pdb=" O ILE G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.744A 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 removed outlier: 3.578A pdb=" N TYR G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 100 removed outlier: 3.505A pdb=" N SER G 97 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE G 201 " --> pdb=" O ARG G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 276 removed outlier: 3.624A pdb=" N GLU G 271 " --> pdb=" O LEU G 267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN G 273 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 41 removed outlier: 3.593A pdb=" N VAL H 38 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA H 39 " --> pdb=" O ILE H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.743A 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 removed outlier: 3.577A pdb=" N TYR H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 100 removed outlier: 3.504A pdb=" N SER H 97 " --> pdb=" O PHE H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE H 201 " --> pdb=" O ARG H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 276 removed outlier: 3.625A pdb=" N GLU H 271 " --> pdb=" O LEU H 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN H 273 " --> pdb=" O LEU H 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS H 274 " --> pdb=" O ALA H 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU H 275 " --> pdb=" O GLU H 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 41 removed outlier: 3.594A pdb=" N VAL I 38 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA I 39 " --> pdb=" O ILE I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.744A 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 removed outlier: 3.577A pdb=" N TYR I 78 " --> pdb=" O SER I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 100 removed outlier: 3.505A pdb=" N SER I 97 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 276 removed outlier: 3.625A pdb=" N GLU I 271 " --> pdb=" O LEU I 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN I 273 " --> pdb=" O LEU I 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS I 274 " --> pdb=" O ALA I 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU I 275 " --> pdb=" O GLU I 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 41 removed outlier: 3.593A pdb=" N VAL J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA J 39 " --> pdb=" O ILE J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.744A 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 removed outlier: 3.576A pdb=" N TYR J 78 " --> pdb=" O SER J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 100 removed outlier: 3.504A pdb=" N SER J 97 " --> pdb=" O PHE J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE J 201 " --> pdb=" O ARG J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 276 removed outlier: 3.624A pdb=" N GLU J 271 " --> pdb=" O LEU J 267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN J 273 " --> pdb=" O LEU J 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS J 274 " --> pdb=" O ALA J 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU J 275 " --> pdb=" O GLU J 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 41 removed outlier: 3.593A pdb=" N VAL K 38 " --> pdb=" O ARG K 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA K 39 " --> pdb=" O ILE K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.744A 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 removed outlier: 3.577A pdb=" N TYR K 78 " --> pdb=" O SER K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 100 removed outlier: 3.504A pdb=" N SER K 97 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE K 201 " --> pdb=" O ARG K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 276 removed outlier: 3.625A pdb=" N GLU K 271 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN K 273 " --> pdb=" O LEU K 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS K 274 " --> pdb=" O ALA K 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU K 275 " --> pdb=" O GLU K 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 41 removed outlier: 3.593A pdb=" N VAL L 38 " --> pdb=" O ARG L 34 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA L 39 " --> pdb=" O ILE L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 removed outlier: 3.841A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.743A 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 removed outlier: 3.577A pdb=" N TYR L 78 " --> pdb=" O SER L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 100 removed outlier: 3.505A pdb=" N SER L 97 " --> pdb=" O PHE L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 221 removed outlier: 3.681A pdb=" N ILE L 201 " --> pdb=" O ARG L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 276 removed outlier: 3.624A pdb=" N GLU L 271 " --> pdb=" O LEU L 267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN L 273 " --> pdb=" O LEU L 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS L 274 " --> pdb=" O ALA L 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU L 275 " --> pdb=" O GLU L 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.653A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.653A 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: 3.653A 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: 3.653A 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: 3.652A 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: 3.653A 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: 3.652A 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: 3.653A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 3060 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: 2.24 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2400 1.31 - 1.44: 4656 1.44 - 1.57: 9960 1.57 - 1.69: 0 1.69 - 1.82: 204 Bond restraints: 17220 Sorted by residual: bond pdb=" C ARG H 34 " pdb=" O ARG H 34 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.29e+01 bond pdb=" C ARG D 34 " pdb=" O ARG D 34 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.28e+01 bond pdb=" C ARG E 34 " pdb=" O ARG E 34 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.27e+01 bond pdb=" C ARG F 34 " pdb=" O ARG F 34 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.26e+01 bond pdb=" C ARG L 34 " pdb=" O ARG L 34 " ideal model delta sigma weight residual 1.236 1.182 0.055 1.15e-02 7.56e+03 2.26e+01 ... (remaining 17215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 21438 2.31 - 4.63: 1192 4.63 - 6.94: 206 6.94 - 9.26: 84 9.26 - 11.57: 24 Bond angle restraints: 22944 Sorted by residual: angle pdb=" N ILE J 37 " pdb=" CA ILE J 37 " pdb=" C ILE J 37 " ideal model delta sigma weight residual 111.00 104.18 6.82 1.09e+00 8.42e-01 3.92e+01 angle pdb=" N ILE C 37 " pdb=" CA ILE C 37 " pdb=" C ILE C 37 " ideal model delta sigma weight residual 111.00 104.18 6.82 1.09e+00 8.42e-01 3.92e+01 angle pdb=" N ILE H 37 " pdb=" CA ILE H 37 " pdb=" C ILE H 37 " ideal model delta sigma weight residual 111.00 104.18 6.82 1.09e+00 8.42e-01 3.91e+01 angle pdb=" N ILE F 37 " pdb=" CA ILE F 37 " pdb=" C ILE F 37 " ideal model delta sigma weight residual 111.00 104.18 6.82 1.09e+00 8.42e-01 3.91e+01 angle pdb=" N ILE K 37 " pdb=" CA ILE K 37 " pdb=" C ILE K 37 " ideal model delta sigma weight residual 111.00 104.20 6.80 1.09e+00 8.42e-01 3.90e+01 ... (remaining 22939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 8456 17.14 - 34.29: 1247 34.29 - 51.43: 533 51.43 - 68.58: 144 68.58 - 85.72: 24 Dihedral angle restraints: 10404 sinusoidal: 4656 harmonic: 5748 Sorted by residual: dihedral pdb=" N LEU E 36 " pdb=" C LEU E 36 " pdb=" CA LEU E 36 " pdb=" CB LEU E 36 " ideal model delta harmonic sigma weight residual 122.80 135.63 -12.83 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" N LEU J 36 " pdb=" C LEU J 36 " pdb=" CA LEU J 36 " pdb=" CB LEU J 36 " ideal model delta harmonic sigma weight residual 122.80 135.62 -12.82 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" N LEU D 36 " pdb=" C LEU D 36 " pdb=" CA LEU D 36 " pdb=" CB LEU D 36 " ideal model delta harmonic sigma weight residual 122.80 135.61 -12.81 0 2.50e+00 1.60e-01 2.63e+01 ... (remaining 10401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2171 0.089 - 0.178: 337 0.178 - 0.267: 36 0.267 - 0.356: 12 0.356 - 0.446: 12 Chirality restraints: 2568 Sorted by residual: chirality pdb=" CA LEU J 36 " pdb=" N LEU J 36 " pdb=" C LEU J 36 " pdb=" CB LEU J 36 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA LEU E 36 " pdb=" N LEU E 36 " pdb=" C LEU E 36 " pdb=" CB LEU E 36 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CA LEU D 36 " pdb=" N LEU D 36 " pdb=" C LEU D 36 " pdb=" CB LEU D 36 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 2565 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 198 " 0.021 2.00e-02 2.50e+03 2.19e-02 8.43e+00 pdb=" CG PHE G 198 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE G 198 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE G 198 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE G 198 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 198 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE G 198 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 198 " -0.021 2.00e-02 2.50e+03 2.19e-02 8.37e+00 pdb=" CG PHE F 198 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE F 198 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 198 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 198 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 198 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F 198 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 198 " 0.022 2.00e-02 2.50e+03 2.18e-02 8.35e+00 pdb=" CG PHE L 198 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE L 198 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE L 198 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE L 198 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE L 198 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE L 198 " 0.001 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3586 2.78 - 3.31: 14738 3.31 - 3.84: 26316 3.84 - 4.37: 30133 4.37 - 4.90: 53806 Nonbonded interactions: 128579 Sorted by model distance: nonbonded pdb=" O ILE B 22 " pdb=" CG1 ILE B 25 " model vdw 2.249 3.440 nonbonded pdb=" O ILE E 22 " pdb=" CG1 ILE E 25 " model vdw 2.250 3.440 nonbonded pdb=" O ILE F 22 " pdb=" CG1 ILE F 25 " model vdw 2.250 3.440 nonbonded pdb=" O ILE C 22 " pdb=" CG1 ILE C 25 " model vdw 2.250 3.440 nonbonded pdb=" O ILE J 22 " pdb=" CG1 ILE J 25 " model vdw 2.250 3.440 ... (remaining 128574 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.070 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.010 0.092 17256 Z= 0.526 Angle : 1.309 11.572 23016 Z= 0.698 Chirality : 0.073 0.446 2568 Planarity : 0.007 0.052 2712 Dihedral : 19.595 85.719 6600 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.35 % Allowed : 25.68 % Favored : 72.97 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.17), residues: 1908 helix: -1.03 (0.12), residues: 1236 sheet: 0.54 (0.41), residues: 144 loop : -0.78 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG J 206 TYR 0.011 0.003 TYR B 67 PHE 0.051 0.003 PHE G 198 TRP 0.008 0.003 TRP B 79 HIS 0.011 0.004 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.01009 (17220) covalent geometry : angle 1.30815 (22944) SS BOND : bond 0.01966 ( 36) SS BOND : angle 1.48587 ( 72) hydrogen bonds : bond 0.18370 ( 1032) hydrogen bonds : angle 6.72810 ( 3060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 291 time to evaluate : 0.577 Fit side-chains REVERT: A 21 MET cc_start: 0.4422 (mpm) cc_final: 0.3764 (pmm) REVERT: A 201 ILE cc_start: 0.8281 (mm) cc_final: 0.8036 (tt) REVERT: B 21 MET cc_start: 0.4785 (mpm) cc_final: 0.4253 (pmm) REVERT: C 21 MET cc_start: 0.4834 (mpm) cc_final: 0.3982 (pmm) REVERT: C 69 ARG cc_start: 0.7427 (tpt170) cc_final: 0.7167 (tpp-160) REVERT: C 201 ILE cc_start: 0.8297 (mm) cc_final: 0.8022 (tt) REVERT: D 21 MET cc_start: 0.4631 (mpm) cc_final: 0.4089 (pmm) REVERT: E 21 MET cc_start: 0.4481 (mpm) cc_final: 0.4134 (pmm) REVERT: F 21 MET cc_start: 0.4498 (mpm) cc_final: 0.3902 (pmm) REVERT: G 21 MET cc_start: 0.4594 (mpm) cc_final: 0.4018 (pmm) REVERT: G 69 ARG cc_start: 0.7479 (tpt170) cc_final: 0.7248 (tpp-160) REVERT: H 21 MET cc_start: 0.4341 (mpm) cc_final: 0.3759 (pmm) REVERT: I 21 MET cc_start: 0.4375 (mpm) cc_final: 0.3774 (pmm) REVERT: J 21 MET cc_start: 0.4845 (mpm) cc_final: 0.4001 (pmm) REVERT: J 69 ARG cc_start: 0.7415 (tpt170) cc_final: 0.7142 (tpp-160) REVERT: J 201 ILE cc_start: 0.8287 (mm) cc_final: 0.8009 (tt) REVERT: K 21 MET cc_start: 0.4643 (mpm) cc_final: 0.3981 (pmm) REVERT: L 21 MET cc_start: 0.4873 (mpm) cc_final: 0.4333 (pmm) outliers start: 24 outliers final: 19 residues processed: 314 average time/residue: 0.5139 time to fit residues: 181.4940 Evaluate side-chains 257 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain L residue 34 ARG Chi-restraints excluded: chain L residue 40 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS B 274 HIS C 274 HIS D 274 HIS E 274 HIS F 274 HIS G 274 HIS H 274 HIS I 274 HIS J 274 HIS K 274 HIS L 274 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.208931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.165650 restraints weight = 15714.110| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.50 r_work: 0.3667 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17256 Z= 0.120 Angle : 0.577 8.292 23016 Z= 0.295 Chirality : 0.040 0.128 2568 Planarity : 0.004 0.036 2712 Dihedral : 14.751 59.826 3134 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.21 % Allowed : 22.30 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 1908 helix: 1.08 (0.14), residues: 1296 sheet: 1.50 (0.36), residues: 120 loop : -0.58 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 69 TYR 0.009 0.001 TYR B 218 PHE 0.026 0.001 PHE A 33 TRP 0.002 0.000 TRP I 79 HIS 0.005 0.002 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00269 (17220) covalent geometry : angle 0.57565 (22944) SS BOND : bond 0.00451 ( 36) SS BOND : angle 0.96296 ( 72) hydrogen bonds : bond 0.04303 ( 1032) hydrogen bonds : angle 3.46726 ( 3060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 254 time to evaluate : 0.536 Fit side-chains REVERT: A 21 MET cc_start: 0.5347 (mpm) cc_final: 0.4181 (pmm) REVERT: B 21 MET cc_start: 0.5329 (mpm) cc_final: 0.3772 (tpp) REVERT: C 21 MET cc_start: 0.5081 (mpm) cc_final: 0.4040 (pmm) REVERT: D 21 MET cc_start: 0.4973 (mpm) cc_final: 0.4042 (pmm) REVERT: E 21 MET cc_start: 0.5032 (mpm) cc_final: 0.3938 (tpp) REVERT: E 274 HIS cc_start: 0.4711 (OUTLIER) cc_final: 0.4458 (m90) REVERT: F 21 MET cc_start: 0.4947 (mpm) cc_final: 0.3736 (tpp) REVERT: F 69 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7338 (tpm-80) REVERT: G 21 MET cc_start: 0.5022 (mpm) cc_final: 0.4115 (pmm) REVERT: H 21 MET cc_start: 0.5186 (mpm) cc_final: 0.4003 (pmm) REVERT: I 21 MET cc_start: 0.4818 (mpm) cc_final: 0.3850 (pmm) REVERT: J 21 MET cc_start: 0.5085 (mpm) cc_final: 0.4033 (pmm) REVERT: J 69 ARG cc_start: 0.8003 (tpt170) cc_final: 0.7753 (tpm170) REVERT: K 21 MET cc_start: 0.5180 (mpm) cc_final: 0.4097 (pmm) REVERT: L 21 MET cc_start: 0.5168 (mpm) cc_final: 0.3798 (tpp) REVERT: L 274 HIS cc_start: 0.4725 (OUTLIER) cc_final: 0.4403 (m90) outliers start: 57 outliers final: 6 residues processed: 291 average time/residue: 0.5100 time to fit residues: 169.6074 Evaluate side-chains 235 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 226 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 274 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 176 optimal weight: 0.0870 chunk 103 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 171 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 HIS ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.238847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.202573 restraints weight = 15519.760| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 1.12 r_work: 0.3995 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17256 Z= 0.140 Angle : 0.587 8.811 23016 Z= 0.294 Chirality : 0.042 0.131 2568 Planarity : 0.004 0.031 2712 Dihedral : 12.663 59.764 3072 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.94 % Allowed : 23.93 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.18), residues: 1908 helix: 1.63 (0.14), residues: 1296 sheet: 1.61 (0.36), residues: 120 loop : -0.84 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 246 TYR 0.010 0.001 TYR F 67 PHE 0.017 0.001 PHE A 33 TRP 0.004 0.001 TRP C 79 HIS 0.012 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00339 (17220) covalent geometry : angle 0.58572 (22944) SS BOND : bond 0.00432 ( 36) SS BOND : angle 0.86706 ( 72) hydrogen bonds : bond 0.04573 ( 1032) hydrogen bonds : angle 3.22770 ( 3060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 203 time to evaluate : 0.638 Fit side-chains REVERT: A 21 MET cc_start: 0.5505 (mpm) cc_final: 0.4250 (pmm) REVERT: A 220 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7491 (tt) REVERT: B 21 MET cc_start: 0.5677 (mpm) cc_final: 0.4067 (tpp) REVERT: C 21 MET cc_start: 0.5186 (mpm) cc_final: 0.4129 (pmm) REVERT: C 69 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7483 (tpm-80) REVERT: C 220 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7460 (tt) REVERT: D 21 MET cc_start: 0.5231 (mpm) cc_final: 0.4233 (pmm) REVERT: D 77 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7141 (mpp-170) REVERT: D 220 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7530 (tt) REVERT: E 21 MET cc_start: 0.5421 (mpm) cc_final: 0.4485 (pmm) REVERT: E 77 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6942 (mpp-170) REVERT: F 21 MET cc_start: 0.5259 (mpm) cc_final: 0.4124 (tpp) REVERT: F 69 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7493 (tpm-80) REVERT: F 220 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7671 (tt) REVERT: G 21 MET cc_start: 0.5097 (mpm) cc_final: 0.4307 (pmm) REVERT: G 69 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7565 (tpm-80) REVERT: H 21 MET cc_start: 0.5578 (mpm) cc_final: 0.4233 (pmm) REVERT: H 220 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7633 (tt) REVERT: I 21 MET cc_start: 0.5012 (mpm) cc_final: 0.4022 (pmm) REVERT: J 21 MET cc_start: 0.5239 (mpm) cc_final: 0.4173 (pmm) REVERT: J 220 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7450 (tt) REVERT: K 21 MET cc_start: 0.5326 (mpm) cc_final: 0.4289 (pmm) REVERT: K 77 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7068 (mpp-170) REVERT: K 220 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7537 (tt) REVERT: L 21 MET cc_start: 0.5478 (mpm) cc_final: 0.4239 (tpp) outliers start: 70 outliers final: 10 residues processed: 259 average time/residue: 0.5073 time to fit residues: 149.4322 Evaluate side-chains 224 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 77 ARG Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 75 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 181 optimal weight: 0.0170 chunk 97 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.207700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.168760 restraints weight = 15526.101| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.42 r_work: 0.3617 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17256 Z= 0.097 Angle : 0.503 8.800 23016 Z= 0.250 Chirality : 0.039 0.121 2568 Planarity : 0.003 0.028 2712 Dihedral : 10.963 58.317 3072 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.38 % Allowed : 26.07 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.19), residues: 1908 helix: 2.15 (0.14), residues: 1296 sheet: 1.80 (0.35), residues: 120 loop : -0.66 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 77 TYR 0.007 0.001 TYR C 67 PHE 0.017 0.001 PHE A 33 TRP 0.002 0.001 TRP D 79 HIS 0.003 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00216 (17220) covalent geometry : angle 0.50238 (22944) SS BOND : bond 0.00184 ( 36) SS BOND : angle 0.65697 ( 72) hydrogen bonds : bond 0.03441 ( 1032) hydrogen bonds : angle 2.96231 ( 3060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 0.497 Fit side-chains REVERT: A 21 MET cc_start: 0.5535 (mpm) cc_final: 0.4407 (pmm) REVERT: A 220 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7088 (tt) REVERT: B 21 MET cc_start: 0.5699 (mpm) cc_final: 0.4045 (tpp) REVERT: C 21 MET cc_start: 0.5427 (mpm) cc_final: 0.4453 (pmm) REVERT: C 69 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7551 (tpm-80) REVERT: D 21 MET cc_start: 0.5302 (mpm) cc_final: 0.4330 (pmm) REVERT: D 220 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7085 (tt) REVERT: E 21 MET cc_start: 0.5754 (mpm) cc_final: 0.4711 (pmm) REVERT: F 21 MET cc_start: 0.5375 (mpm) cc_final: 0.4112 (tpp) REVERT: G 21 MET cc_start: 0.5436 (mpm) cc_final: 0.4509 (pmm) REVERT: G 69 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7612 (tpm-80) REVERT: H 21 MET cc_start: 0.5496 (mpm) cc_final: 0.4406 (pmm) REVERT: H 220 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7042 (tt) REVERT: I 21 MET cc_start: 0.5510 (mpm) cc_final: 0.4490 (pmm) REVERT: J 21 MET cc_start: 0.5419 (mpm) cc_final: 0.4469 (pmm) REVERT: K 21 MET cc_start: 0.5490 (mpm) cc_final: 0.4477 (pmm) REVERT: K 220 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7124 (tt) REVERT: L 21 MET cc_start: 0.5867 (mpm) cc_final: 0.4722 (pmm) outliers start: 60 outliers final: 7 residues processed: 274 average time/residue: 0.3990 time to fit residues: 126.9276 Evaluate side-chains 230 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 36 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 25 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 HIS ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.204602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.163026 restraints weight = 15806.381| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.09 r_work: 0.3679 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17256 Z= 0.103 Angle : 0.526 10.429 23016 Z= 0.255 Chirality : 0.039 0.124 2568 Planarity : 0.003 0.026 2712 Dihedral : 10.239 59.268 3072 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.17 % Allowed : 26.01 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.19), residues: 1908 helix: 2.30 (0.14), residues: 1296 sheet: 1.99 (0.35), residues: 120 loop : -0.54 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 77 TYR 0.008 0.001 TYR G 67 PHE 0.014 0.001 PHE A 33 TRP 0.003 0.001 TRP I 79 HIS 0.002 0.001 HIS J 99 Details of bonding type rmsd covalent geometry : bond 0.00237 (17220) covalent geometry : angle 0.52564 (22944) SS BOND : bond 0.00297 ( 36) SS BOND : angle 0.63233 ( 72) hydrogen bonds : bond 0.03570 ( 1032) hydrogen bonds : angle 2.90451 ( 3060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 208 time to evaluate : 0.551 Fit side-chains REVERT: A 21 MET cc_start: 0.5769 (mpm) cc_final: 0.4671 (pmm) REVERT: A 36 LEU cc_start: 0.6880 (tt) cc_final: 0.6638 (tp) REVERT: A 220 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7269 (tt) REVERT: B 21 MET cc_start: 0.5631 (mpm) cc_final: 0.4014 (tpp) REVERT: C 21 MET cc_start: 0.5573 (mpm) cc_final: 0.4644 (pmm) REVERT: D 21 MET cc_start: 0.5707 (mpm) cc_final: 0.4688 (pmm) REVERT: D 220 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7185 (tt) REVERT: E 21 MET cc_start: 0.5879 (mpm) cc_final: 0.4756 (pmm) REVERT: F 21 MET cc_start: 0.5726 (mpm) cc_final: 0.4756 (pmm) REVERT: F 22 ILE cc_start: 0.5591 (OUTLIER) cc_final: 0.5311 (pt) REVERT: G 21 MET cc_start: 0.5383 (mpm) cc_final: 0.4610 (pmm) REVERT: G 22 ILE cc_start: 0.5640 (OUTLIER) cc_final: 0.5359 (pt) REVERT: G 69 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7546 (tpm-80) REVERT: H 21 MET cc_start: 0.5688 (mpm) cc_final: 0.4652 (pmm) REVERT: H 220 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7204 (tt) REVERT: I 21 MET cc_start: 0.5770 (mpm) cc_final: 0.4888 (pmm) REVERT: J 21 MET cc_start: 0.5551 (mpm) cc_final: 0.4604 (pmm) REVERT: K 21 MET cc_start: 0.5673 (mpm) cc_final: 0.4668 (pmm) REVERT: K 220 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7255 (tt) REVERT: L 21 MET cc_start: 0.5814 (mpm) cc_final: 0.4718 (pmm) outliers start: 74 outliers final: 15 residues processed: 267 average time/residue: 0.4150 time to fit residues: 129.3172 Evaluate side-chains 221 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 36 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.202284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161843 restraints weight = 15661.904| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.14 r_work: 0.3630 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17256 Z= 0.126 Angle : 0.575 9.972 23016 Z= 0.281 Chirality : 0.041 0.126 2568 Planarity : 0.004 0.026 2712 Dihedral : 10.354 59.742 3072 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.72 % Allowed : 27.25 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.19), residues: 1908 helix: 2.13 (0.14), residues: 1296 sheet: 1.22 (0.39), residues: 132 loop : -0.35 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 246 TYR 0.010 0.001 TYR F 67 PHE 0.013 0.001 PHE A 33 TRP 0.004 0.001 TRP L 79 HIS 0.002 0.001 HIS K 99 Details of bonding type rmsd covalent geometry : bond 0.00302 (17220) covalent geometry : angle 0.57409 (22944) SS BOND : bond 0.00427 ( 36) SS BOND : angle 0.74109 ( 72) hydrogen bonds : bond 0.03963 ( 1032) hydrogen bonds : angle 2.97268 ( 3060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 0.606 Fit side-chains REVERT: A 21 MET cc_start: 0.5792 (mpm) cc_final: 0.4619 (pmm) REVERT: A 22 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.5322 (pt) REVERT: A 220 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7226 (tt) REVERT: B 21 MET cc_start: 0.5804 (mpm) cc_final: 0.4730 (pmm) REVERT: C 21 MET cc_start: 0.5624 (mpm) cc_final: 0.4649 (pmm) REVERT: C 22 ILE cc_start: 0.5602 (OUTLIER) cc_final: 0.5359 (pt) REVERT: C 69 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7566 (tpm-80) REVERT: C 220 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.6909 (tt) REVERT: C 253 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: D 21 MET cc_start: 0.5689 (mpm) cc_final: 0.4693 (pmm) REVERT: D 22 ILE cc_start: 0.5673 (OUTLIER) cc_final: 0.5445 (pt) REVERT: D 220 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7229 (tt) REVERT: E 21 MET cc_start: 0.5880 (mpm) cc_final: 0.4748 (pmm) REVERT: E 253 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: F 21 MET cc_start: 0.5796 (mpm) cc_final: 0.4787 (pmm) REVERT: G 21 MET cc_start: 0.5728 (mpm) cc_final: 0.4772 (pmm) REVERT: G 69 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7618 (tpm-80) REVERT: H 21 MET cc_start: 0.5808 (mpm) cc_final: 0.4725 (pmm) REVERT: H 22 ILE cc_start: 0.5697 (OUTLIER) cc_final: 0.5440 (pt) REVERT: H 220 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7256 (tt) REVERT: I 21 MET cc_start: 0.5838 (mpm) cc_final: 0.4909 (pmm) REVERT: J 21 MET cc_start: 0.5575 (mpm) cc_final: 0.4678 (pmm) REVERT: J 22 ILE cc_start: 0.5593 (OUTLIER) cc_final: 0.5361 (pt) REVERT: J 220 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.6944 (tt) REVERT: J 253 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: K 21 MET cc_start: 0.5622 (mpm) cc_final: 0.4622 (pmm) REVERT: K 22 ILE cc_start: 0.5463 (OUTLIER) cc_final: 0.5253 (pt) REVERT: K 220 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7258 (tt) REVERT: L 21 MET cc_start: 0.5884 (mpm) cc_final: 0.4752 (pmm) outliers start: 66 outliers final: 16 residues processed: 238 average time/residue: 0.4520 time to fit residues: 125.0086 Evaluate side-chains 207 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 36 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 149 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.202843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.164109 restraints weight = 15639.102| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.24 r_work: 0.3634 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17256 Z= 0.118 Angle : 0.543 8.886 23016 Z= 0.267 Chirality : 0.040 0.127 2568 Planarity : 0.003 0.025 2712 Dihedral : 10.017 59.381 3072 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.98 % Allowed : 28.10 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.19), residues: 1908 helix: 2.21 (0.14), residues: 1296 sheet: 1.41 (0.40), residues: 132 loop : -0.32 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 246 TYR 0.017 0.001 TYR F 67 PHE 0.013 0.001 PHE A 33 TRP 0.004 0.001 TRP F 79 HIS 0.002 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00280 (17220) covalent geometry : angle 0.54193 (22944) SS BOND : bond 0.00384 ( 36) SS BOND : angle 0.72226 ( 72) hydrogen bonds : bond 0.03752 ( 1032) hydrogen bonds : angle 2.93775 ( 3060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.642 Fit side-chains REVERT: A 21 MET cc_start: 0.5714 (mpm) cc_final: 0.4627 (pmm) REVERT: A 22 ILE cc_start: 0.5636 (OUTLIER) cc_final: 0.5354 (pt) REVERT: A 220 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7329 (tt) REVERT: B 21 MET cc_start: 0.5890 (mpm) cc_final: 0.4302 (tpp) REVERT: C 21 MET cc_start: 0.5597 (mpm) cc_final: 0.4659 (pmm) REVERT: C 22 ILE cc_start: 0.5632 (OUTLIER) cc_final: 0.5415 (pt) REVERT: C 69 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7598 (tpm-80) REVERT: C 220 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7008 (tt) REVERT: D 21 MET cc_start: 0.5611 (mpm) cc_final: 0.4638 (pmm) REVERT: D 22 ILE cc_start: 0.5618 (OUTLIER) cc_final: 0.5396 (pt) REVERT: D 220 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7252 (tt) REVERT: E 21 MET cc_start: 0.5926 (mpm) cc_final: 0.4768 (pmm) REVERT: F 21 MET cc_start: 0.5824 (mpm) cc_final: 0.4750 (pmm) REVERT: F 22 ILE cc_start: 0.5651 (OUTLIER) cc_final: 0.5412 (pt) REVERT: G 21 MET cc_start: 0.5667 (mpm) cc_final: 0.4720 (pmm) REVERT: G 22 ILE cc_start: 0.5619 (OUTLIER) cc_final: 0.5381 (pt) REVERT: G 69 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7608 (tpm-80) REVERT: H 21 MET cc_start: 0.5823 (mpm) cc_final: 0.4736 (pmm) REVERT: H 22 ILE cc_start: 0.5679 (OUTLIER) cc_final: 0.5437 (pt) REVERT: H 220 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7214 (tt) REVERT: I 21 MET cc_start: 0.5883 (mpm) cc_final: 0.4917 (pmm) REVERT: J 21 MET cc_start: 0.5597 (mpm) cc_final: 0.4624 (pmm) REVERT: J 22 ILE cc_start: 0.5613 (OUTLIER) cc_final: 0.5380 (pt) REVERT: J 220 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.6993 (tt) REVERT: K 21 MET cc_start: 0.5614 (mpm) cc_final: 0.4624 (pmm) REVERT: K 220 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7277 (tt) REVERT: L 21 MET cc_start: 0.5947 (mpm) cc_final: 0.4784 (pmm) outliers start: 53 outliers final: 15 residues processed: 226 average time/residue: 0.4329 time to fit residues: 113.8380 Evaluate side-chains 208 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 36 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.232416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.196886 restraints weight = 15418.580| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 1.09 r_work: 0.3979 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 17256 Z= 0.265 Angle : 0.722 10.091 23016 Z= 0.358 Chirality : 0.049 0.171 2568 Planarity : 0.005 0.031 2712 Dihedral : 11.554 59.201 3072 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.72 % Allowed : 27.53 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.19), residues: 1908 helix: 1.39 (0.14), residues: 1296 sheet: 1.08 (0.37), residues: 144 loop : -0.23 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 246 TYR 0.031 0.003 TYR J 67 PHE 0.015 0.002 PHE G 256 TRP 0.012 0.003 TRP L 79 HIS 0.004 0.001 HIS J 75 Details of bonding type rmsd covalent geometry : bond 0.00671 (17220) covalent geometry : angle 0.71761 (22944) SS BOND : bond 0.01043 ( 36) SS BOND : angle 1.54511 ( 72) hydrogen bonds : bond 0.05741 ( 1032) hydrogen bonds : angle 3.45870 ( 3060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 0.620 Fit side-chains REVERT: A 21 MET cc_start: 0.5603 (mpm) cc_final: 0.4627 (pmm) REVERT: A 22 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5632 (pt) REVERT: A 220 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7738 (tt) REVERT: B 21 MET cc_start: 0.5846 (mpm) cc_final: 0.4434 (tpp) REVERT: C 21 MET cc_start: 0.5593 (mpm) cc_final: 0.4746 (pmm) REVERT: C 22 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5577 (pt) REVERT: C 69 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7684 (tpm-80) REVERT: C 220 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7452 (tt) REVERT: D 21 MET cc_start: 0.5571 (mpm) cc_final: 0.4626 (pmm) REVERT: D 220 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7722 (tt) REVERT: D 272 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5788 (tm) REVERT: E 21 MET cc_start: 0.5756 (mpm) cc_final: 0.4754 (pmm) REVERT: E 274 HIS cc_start: 0.5334 (OUTLIER) cc_final: 0.4867 (m-70) REVERT: F 21 MET cc_start: 0.5768 (mpm) cc_final: 0.4295 (tpp) REVERT: F 22 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5792 (pt) REVERT: F 220 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7779 (tt) REVERT: G 21 MET cc_start: 0.5673 (mpm) cc_final: 0.4330 (tpp) REVERT: G 22 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5653 (pt) REVERT: G 69 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7654 (tpm-80) REVERT: G 220 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7775 (tt) REVERT: H 21 MET cc_start: 0.5664 (mpm) cc_final: 0.4694 (pmm) REVERT: H 22 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.5694 (pt) REVERT: H 220 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7743 (tt) REVERT: I 21 MET cc_start: 0.5824 (mpm) cc_final: 0.4931 (pmm) REVERT: J 21 MET cc_start: 0.5609 (mpm) cc_final: 0.4728 (pmm) REVERT: J 22 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5640 (pt) REVERT: J 220 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7488 (tt) REVERT: K 21 MET cc_start: 0.5600 (mpm) cc_final: 0.4670 (pmm) REVERT: K 220 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7703 (tt) REVERT: L 21 MET cc_start: 0.5941 (mpm) cc_final: 0.4505 (tpp) REVERT: L 274 HIS cc_start: 0.5364 (OUTLIER) cc_final: 0.4878 (m-70) outliers start: 66 outliers final: 22 residues processed: 252 average time/residue: 0.4076 time to fit residues: 120.1512 Evaluate side-chains 222 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 274 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 175 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.0050 chunk 5 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.211094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.172333 restraints weight = 15622.340| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.24 r_work: 0.3627 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17256 Z= 0.096 Angle : 0.504 8.501 23016 Z= 0.251 Chirality : 0.038 0.121 2568 Planarity : 0.004 0.027 2712 Dihedral : 9.298 59.796 3072 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.91 % Allowed : 29.79 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.19), residues: 1908 helix: 2.24 (0.14), residues: 1296 sheet: 1.58 (0.40), residues: 132 loop : -0.35 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 77 TYR 0.018 0.001 TYR J 67 PHE 0.014 0.001 PHE A 33 TRP 0.001 0.000 TRP B 79 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00211 (17220) covalent geometry : angle 0.50305 (22944) SS BOND : bond 0.00113 ( 36) SS BOND : angle 0.74692 ( 72) hydrogen bonds : bond 0.03234 ( 1032) hydrogen bonds : angle 2.92142 ( 3060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.509 Fit side-chains REVERT: A 21 MET cc_start: 0.5704 (mpm) cc_final: 0.4584 (pmm) REVERT: A 22 ILE cc_start: 0.5563 (OUTLIER) cc_final: 0.5319 (pt) REVERT: A 220 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7072 (tt) REVERT: A 254 LEU cc_start: 0.7681 (mt) cc_final: 0.7453 (tp) REVERT: B 21 MET cc_start: 0.5958 (mpm) cc_final: 0.4350 (tpp) REVERT: C 21 MET cc_start: 0.5652 (mpm) cc_final: 0.4653 (pmm) REVERT: C 22 ILE cc_start: 0.5561 (OUTLIER) cc_final: 0.5342 (pt) REVERT: D 21 MET cc_start: 0.5518 (mpm) cc_final: 0.4534 (pmm) REVERT: D 220 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7045 (tt) REVERT: D 254 LEU cc_start: 0.7598 (mt) cc_final: 0.7372 (tp) REVERT: E 21 MET cc_start: 0.5682 (mpm) cc_final: 0.4584 (pmm) REVERT: E 274 HIS cc_start: 0.5557 (OUTLIER) cc_final: 0.5045 (m-70) REVERT: F 21 MET cc_start: 0.5942 (mpm) cc_final: 0.4343 (tpp) REVERT: G 21 MET cc_start: 0.5696 (mpm) cc_final: 0.4691 (pmm) REVERT: G 22 ILE cc_start: 0.5587 (OUTLIER) cc_final: 0.5342 (pt) REVERT: H 21 MET cc_start: 0.5663 (mpm) cc_final: 0.4599 (pmm) REVERT: H 220 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7077 (tt) REVERT: I 21 MET cc_start: 0.5881 (mpm) cc_final: 0.4868 (pmm) REVERT: J 21 MET cc_start: 0.5710 (mpm) cc_final: 0.4680 (pmm) REVERT: J 22 ILE cc_start: 0.5537 (OUTLIER) cc_final: 0.5315 (pt) REVERT: K 21 MET cc_start: 0.5585 (mpm) cc_final: 0.4622 (pmm) REVERT: K 220 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7073 (tt) REVERT: K 254 LEU cc_start: 0.7647 (mt) cc_final: 0.7423 (tp) REVERT: L 21 MET cc_start: 0.5809 (mpm) cc_final: 0.4056 (tpp) REVERT: L 274 HIS cc_start: 0.5577 (OUTLIER) cc_final: 0.5062 (m-70) outliers start: 34 outliers final: 10 residues processed: 252 average time/residue: 0.3880 time to fit residues: 114.5748 Evaluate side-chains 211 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 274 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 147 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.235595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.199266 restraints weight = 15234.322| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 1.08 r_work: 0.4009 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17256 Z= 0.182 Angle : 0.625 10.637 23016 Z= 0.309 Chirality : 0.044 0.143 2568 Planarity : 0.004 0.028 2712 Dihedral : 10.372 59.899 3072 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.20 % Allowed : 29.45 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 1908 helix: 1.86 (0.14), residues: 1296 sheet: 1.47 (0.41), residues: 132 loop : -0.34 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 246 TYR 0.025 0.002 TYR F 67 PHE 0.012 0.002 PHE A 33 TRP 0.008 0.002 TRP E 79 HIS 0.002 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00457 (17220) covalent geometry : angle 0.62329 (22944) SS BOND : bond 0.00712 ( 36) SS BOND : angle 1.07988 ( 72) hydrogen bonds : bond 0.04754 ( 1032) hydrogen bonds : angle 3.18702 ( 3060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.652 Fit side-chains REVERT: A 21 MET cc_start: 0.5743 (mpm) cc_final: 0.4697 (pmm) REVERT: A 22 ILE cc_start: 0.5807 (OUTLIER) cc_final: 0.5575 (pt) REVERT: A 220 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7660 (tt) REVERT: B 21 MET cc_start: 0.5962 (mpm) cc_final: 0.4372 (tpp) REVERT: C 21 MET cc_start: 0.5545 (mpm) cc_final: 0.4636 (pmm) REVERT: C 22 ILE cc_start: 0.5798 (OUTLIER) cc_final: 0.5585 (pt) REVERT: D 21 MET cc_start: 0.5610 (mpm) cc_final: 0.4632 (pmm) REVERT: D 220 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7625 (tt) REVERT: E 21 MET cc_start: 0.5820 (mpm) cc_final: 0.4445 (tpp) REVERT: E 274 HIS cc_start: 0.5535 (OUTLIER) cc_final: 0.5088 (m-70) REVERT: F 21 MET cc_start: 0.5895 (mpm) cc_final: 0.4334 (tpp) REVERT: G 21 MET cc_start: 0.5860 (mpm) cc_final: 0.4313 (tpp) REVERT: H 21 MET cc_start: 0.5739 (mpm) cc_final: 0.4685 (pmm) REVERT: H 220 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7674 (tt) REVERT: I 21 MET cc_start: 0.5970 (mpm) cc_final: 0.4952 (pmm) REVERT: J 21 MET cc_start: 0.5737 (mpm) cc_final: 0.4753 (pmm) REVERT: J 22 ILE cc_start: 0.5735 (OUTLIER) cc_final: 0.5511 (pt) REVERT: K 21 MET cc_start: 0.5580 (mpm) cc_final: 0.4599 (pmm) REVERT: K 220 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7655 (tt) REVERT: L 21 MET cc_start: 0.5873 (mpm) cc_final: 0.4314 (tpp) REVERT: L 274 HIS cc_start: 0.5583 (OUTLIER) cc_final: 0.5105 (m-70) outliers start: 39 outliers final: 14 residues processed: 216 average time/residue: 0.4098 time to fit residues: 103.1014 Evaluate side-chains 200 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 274 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 91 optimal weight: 0.0970 chunk 158 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.206096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.166887 restraints weight = 15478.166| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.25 r_work: 0.3592 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17256 Z= 0.117 Angle : 0.549 9.732 23016 Z= 0.270 Chirality : 0.040 0.127 2568 Planarity : 0.004 0.026 2712 Dihedral : 9.606 59.955 3072 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.63 % Allowed : 30.12 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.19), residues: 1908 helix: 2.17 (0.14), residues: 1296 sheet: 1.64 (0.42), residues: 132 loop : -0.32 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 246 TYR 0.018 0.001 TYR F 67 PHE 0.013 0.001 PHE A 33 TRP 0.003 0.001 TRP E 79 HIS 0.002 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00275 (17220) covalent geometry : angle 0.54862 (22944) SS BOND : bond 0.00344 ( 36) SS BOND : angle 0.77931 ( 72) hydrogen bonds : bond 0.03800 ( 1032) hydrogen bonds : angle 3.00751 ( 3060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5053.19 seconds wall clock time: 86 minutes 55.17 seconds (5215.17 seconds total)