Starting phenix.real_space_refine on Tue Nov 19 11:54:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/11_2024/7xl8_33274_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/11_2024/7xl8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/11_2024/7xl8_33274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/11_2024/7xl8_33274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/11_2024/7xl8_33274_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/11_2024/7xl8_33274_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 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-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 10.09, per 1000 atoms: 0.60 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: 4.41 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.65 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: 4.86 Time building geometry restraints manager: 5.09 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: 0.00 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: 3.120 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.600 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.760 ------------------------------------------------------------------------------- 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 17220 Z= 0.639 Angle : 1.308 11.572 22944 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (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 TRP 0.008 0.003 TRP B 79 HIS 0.011 0.004 HIS C 274 PHE 0.051 0.003 PHE G 198 TYR 0.011 0.003 TYR B 67 ARG 0.011 0.002 ARG J 206 *********************** 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 : 1.773 Fit side-chains REVERT: A 21 MET cc_start: 0.4421 (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: 0.7416 (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: 0.4642 (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: 1.1571 time to fit residues: 409.9179 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 : 1.852 ------------------------------------------------------------------------------- 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 162 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 0.0970 chunk 150 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17220 Z= 0.168 Angle : 0.578 8.491 22944 Z= 0.295 Chirality : 0.040 0.128 2568 Planarity : 0.005 0.035 2712 Dihedral : 14.838 59.977 3134 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.15 % Allowed : 22.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 1908 helix: 1.09 (0.14), residues: 1296 sheet: 1.47 (0.35), residues: 120 loop : -0.55 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 79 HIS 0.005 0.002 HIS D 99 PHE 0.028 0.001 PHE A 33 TYR 0.009 0.001 TYR B 218 ARG 0.001 0.000 ARG F 233 *********************** 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 314 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 1.784 Fit side-chains REVERT: A 21 MET cc_start: 0.5154 (mpm) cc_final: 0.4061 (pmm) REVERT: A 69 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7560 (tpp-160) REVERT: B 21 MET cc_start: 0.5338 (mpm) cc_final: 0.3998 (tpp) REVERT: C 21 MET cc_start: 0.4899 (mpm) cc_final: 0.3916 (pmm) REVERT: D 21 MET cc_start: 0.4791 (mpm) cc_final: 0.4050 (pmm) REVERT: E 21 MET cc_start: 0.5007 (mpm) cc_final: 0.4218 (tpp) REVERT: E 69 ARG cc_start: 0.7854 (tpp-160) cc_final: 0.7646 (tpp-160) REVERT: E 274 HIS cc_start: 0.4272 (OUTLIER) cc_final: 0.4054 (m90) REVERT: F 21 MET cc_start: 0.5046 (mpm) cc_final: 0.3907 (tpp) REVERT: F 69 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6718 (tpm-80) REVERT: G 21 MET cc_start: 0.4998 (mpm) cc_final: 0.4229 (pmm) REVERT: H 21 MET cc_start: 0.5129 (mpm) cc_final: 0.4034 (pmm) REVERT: H 69 ARG cc_start: 0.7756 (tpp-160) cc_final: 0.7540 (tpp-160) REVERT: I 21 MET cc_start: 0.4759 (mpm) cc_final: 0.3872 (pmm) REVERT: J 21 MET cc_start: 0.5036 (mpm) cc_final: 0.4075 (pmm) REVERT: K 21 MET cc_start: 0.5095 (mpm) cc_final: 0.4154 (pmm) REVERT: K 69 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7563 (tpp-160) REVERT: K 272 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5695 (tt) REVERT: L 21 MET cc_start: 0.5192 (mpm) cc_final: 0.4054 (tpp) REVERT: L 274 HIS cc_start: 0.4307 (OUTLIER) cc_final: 0.4013 (m90) outliers start: 56 outliers final: 6 residues processed: 294 average time/residue: 1.0022 time to fit residues: 337.1976 Evaluate side-chains 237 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 227 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 K residue 272 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 96 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 0.1980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17220 Z= 0.229 Angle : 0.597 9.148 22944 Z= 0.299 Chirality : 0.042 0.138 2568 Planarity : 0.004 0.031 2712 Dihedral : 12.846 59.413 3072 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.94 % Allowed : 23.54 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.18), residues: 1908 helix: 1.57 (0.14), residues: 1296 sheet: 1.60 (0.36), residues: 120 loop : -0.83 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 79 HIS 0.011 0.001 HIS L 274 PHE 0.017 0.001 PHE A 33 TYR 0.009 0.001 TYR G 67 ARG 0.001 0.000 ARG A 246 *********************** 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 282 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 1.839 Fit side-chains REVERT: A 21 MET cc_start: 0.5445 (mpm) cc_final: 0.4250 (pmm) REVERT: A 69 ARG cc_start: 0.7879 (tpp-160) cc_final: 0.7637 (tpp-160) REVERT: A 220 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7013 (tt) REVERT: B 21 MET cc_start: 0.5590 (mpm) cc_final: 0.4050 (tpp) REVERT: C 21 MET cc_start: 0.5122 (mpm) cc_final: 0.4131 (pmm) REVERT: C 220 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.6780 (tt) REVERT: D 21 MET cc_start: 0.5223 (mpm) cc_final: 0.4254 (pmm) REVERT: D 77 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6637 (mpp-170) REVERT: D 220 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6986 (tt) REVERT: E 21 MET cc_start: 0.5323 (mpm) cc_final: 0.4317 (tpp) REVERT: E 69 ARG cc_start: 0.7864 (tpp-160) cc_final: 0.7659 (tpp-160) REVERT: E 77 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6474 (mpp-170) REVERT: F 21 MET cc_start: 0.5146 (mpm) cc_final: 0.4184 (tpp) REVERT: F 69 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6783 (tpm-80) REVERT: F 220 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6987 (tt) REVERT: G 21 MET cc_start: 0.4977 (mpm) cc_final: 0.4284 (pmm) REVERT: G 69 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6803 (tpm-80) REVERT: G 220 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.6770 (tt) REVERT: G 249 GLU cc_start: 0.7289 (tt0) cc_final: 0.7058 (tt0) REVERT: H 21 MET cc_start: 0.5498 (mpm) cc_final: 0.4235 (pmm) REVERT: H 69 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7634 (tpp-160) REVERT: H 77 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6588 (mpp-170) REVERT: H 220 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7057 (tt) REVERT: I 21 MET cc_start: 0.4898 (mpm) cc_final: 0.4026 (pmm) REVERT: J 21 MET cc_start: 0.5132 (mpm) cc_final: 0.4124 (pmm) REVERT: J 69 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6784 (tpm-80) REVERT: J 220 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6764 (tt) REVERT: K 21 MET cc_start: 0.5236 (mpm) cc_final: 0.4290 (pmm) REVERT: K 69 ARG cc_start: 0.7841 (tpp-160) cc_final: 0.7632 (tpp-160) REVERT: K 77 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6590 (mpp-170) REVERT: K 220 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.6982 (tt) REVERT: L 21 MET cc_start: 0.5388 (mpm) cc_final: 0.4265 (tpp) outliers start: 70 outliers final: 11 residues processed: 269 average time/residue: 1.1200 time to fit residues: 341.3693 Evaluate side-chains 230 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 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 57 THR 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 G residue 220 LEU Chi-restraints excluded: chain H residue 77 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 69 ARG 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 172 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 117 optimal weight: 0.0050 chunk 175 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- 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** B 274 HIS ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17220 Z= 0.239 Angle : 0.587 9.137 22944 Z= 0.291 Chirality : 0.042 0.128 2568 Planarity : 0.004 0.029 2712 Dihedral : 11.761 59.506 3072 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.22 % Allowed : 24.83 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.19), residues: 1908 helix: 1.73 (0.14), residues: 1296 sheet: 1.76 (0.35), residues: 120 loop : -0.75 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 79 HIS 0.002 0.001 HIS F 99 PHE 0.016 0.001 PHE A 33 TYR 0.011 0.002 TYR F 67 ARG 0.002 0.000 ARG L 246 *********************** 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 266 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 191 time to evaluate : 1.892 Fit side-chains REVERT: A 21 MET cc_start: 0.5397 (mpm) cc_final: 0.4314 (pmm) REVERT: A 220 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.6900 (tt) REVERT: B 21 MET cc_start: 0.5589 (mpm) cc_final: 0.4125 (tpp) REVERT: C 21 MET cc_start: 0.5178 (mpm) cc_final: 0.4256 (pmm) REVERT: C 220 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6495 (tt) REVERT: C 253 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6591 (m-80) REVERT: D 21 MET cc_start: 0.5273 (mpm) cc_final: 0.4300 (pmm) REVERT: D 220 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.6913 (tt) REVERT: E 21 MET cc_start: 0.5619 (mpm) cc_final: 0.4725 (pmm) REVERT: E 253 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: F 21 MET cc_start: 0.5267 (mpm) cc_final: 0.4313 (tpp) REVERT: F 69 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6714 (tpm-80) REVERT: F 220 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7148 (tt) REVERT: G 21 MET cc_start: 0.5170 (mpm) cc_final: 0.4394 (pmm) REVERT: G 69 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6796 (tpm-80) REVERT: G 220 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.6444 (tt) REVERT: H 21 MET cc_start: 0.5432 (mpm) cc_final: 0.4402 (pmm) REVERT: H 220 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6921 (tt) REVERT: I 21 MET cc_start: 0.5112 (mpm) cc_final: 0.4257 (pmm) REVERT: I 220 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7321 (tt) REVERT: J 21 MET cc_start: 0.5180 (mpm) cc_final: 0.4254 (pmm) REVERT: J 69 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6752 (tpm-80) REVERT: J 220 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6480 (tt) REVERT: J 253 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6589 (m-80) REVERT: K 21 MET cc_start: 0.5370 (mpm) cc_final: 0.4507 (pmm) REVERT: K 220 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.6903 (tt) REVERT: L 21 MET cc_start: 0.5696 (mpm) cc_final: 0.4677 (pmm) outliers start: 75 outliers final: 18 residues processed: 250 average time/residue: 1.0606 time to fit residues: 302.2720 Evaluate side-chains 222 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 253 PHE 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 57 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 220 LEU 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 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain J residue 253 PHE 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 25 ILE Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** B 274 HIS H 274 HIS ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17220 Z= 0.158 Angle : 0.524 8.844 22944 Z= 0.258 Chirality : 0.039 0.123 2568 Planarity : 0.004 0.028 2712 Dihedral : 10.596 59.770 3072 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.22 % Allowed : 25.51 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 1908 helix: 2.12 (0.14), residues: 1296 sheet: 1.81 (0.35), residues: 120 loop : -0.58 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 79 HIS 0.002 0.001 HIS J 99 PHE 0.015 0.001 PHE A 33 TYR 0.008 0.001 TYR J 67 ARG 0.001 0.000 ARG H 77 *********************** 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 276 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 201 time to evaluate : 1.804 Fit side-chains REVERT: A 21 MET cc_start: 0.5723 (mpm) cc_final: 0.4680 (pmm) REVERT: A 220 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6914 (tt) REVERT: B 21 MET cc_start: 0.5531 (mpm) cc_final: 0.4041 (tpp) REVERT: C 21 MET cc_start: 0.5313 (mpm) cc_final: 0.4483 (pmm) REVERT: D 21 MET cc_start: 0.5349 (mpm) cc_final: 0.4517 (pmm) REVERT: D 220 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6916 (tt) REVERT: E 21 MET cc_start: 0.5602 (mpm) cc_final: 0.4668 (pmm) REVERT: F 21 MET cc_start: 0.5340 (mpm) cc_final: 0.4184 (tpp) REVERT: F 69 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6701 (tpm-80) REVERT: G 21 MET cc_start: 0.5245 (mpm) cc_final: 0.4574 (pmm) REVERT: G 69 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6714 (tpm-80) REVERT: H 21 MET cc_start: 0.5663 (mpm) cc_final: 0.4625 (pmm) REVERT: H 220 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.6928 (tt) REVERT: I 21 MET cc_start: 0.5675 (mpm) cc_final: 0.4826 (pmm) REVERT: J 21 MET cc_start: 0.5311 (mpm) cc_final: 0.4472 (pmm) REVERT: J 69 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6706 (tpm-80) REVERT: K 21 MET cc_start: 0.5547 (mpm) cc_final: 0.4679 (pmm) REVERT: K 220 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6921 (tt) REVERT: L 21 MET cc_start: 0.5681 (mpm) cc_final: 0.4657 (pmm) outliers start: 75 outliers final: 14 residues processed: 259 average time/residue: 0.9346 time to fit residues: 280.3707 Evaluate side-chains 216 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 36 LEU 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 69 ARG 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 69 ARG 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 62 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17220 Z= 0.193 Angle : 0.573 8.983 22944 Z= 0.283 Chirality : 0.041 0.126 2568 Planarity : 0.004 0.027 2712 Dihedral : 10.448 59.598 3072 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.15 % Allowed : 27.42 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.19), residues: 1908 helix: 2.05 (0.14), residues: 1296 sheet: 1.89 (0.36), residues: 120 loop : -0.56 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.002 0.001 HIS J 99 PHE 0.014 0.001 PHE A 33 TYR 0.010 0.001 TYR J 67 ARG 0.001 0.000 ARG H 77 *********************** 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 242 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 1.860 Fit side-chains REVERT: A 21 MET cc_start: 0.5600 (mpm) cc_final: 0.4618 (pmm) REVERT: A 22 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5550 (pt) REVERT: A 220 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6898 (tt) REVERT: B 21 MET cc_start: 0.5697 (mpm) cc_final: 0.4316 (tpp) REVERT: C 21 MET cc_start: 0.5570 (mpm) cc_final: 0.4682 (pmm) REVERT: D 21 MET cc_start: 0.5518 (mpm) cc_final: 0.4636 (pmm) REVERT: D 22 ILE cc_start: 0.5879 (OUTLIER) cc_final: 0.5646 (pt) REVERT: D 220 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6887 (tt) REVERT: E 21 MET cc_start: 0.5627 (mpm) cc_final: 0.4676 (pmm) REVERT: E 253 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: F 21 MET cc_start: 0.5584 (mpm) cc_final: 0.4745 (pmm) REVERT: F 22 ILE cc_start: 0.5864 (OUTLIER) cc_final: 0.5624 (pt) REVERT: F 69 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6719 (tpm-80) REVERT: G 21 MET cc_start: 0.5633 (mpm) cc_final: 0.4808 (pmm) REVERT: G 69 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6753 (tpm-80) REVERT: G 253 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: H 21 MET cc_start: 0.5619 (mpm) cc_final: 0.4714 (pmm) REVERT: H 220 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6919 (tt) REVERT: I 21 MET cc_start: 0.5699 (mpm) cc_final: 0.4840 (pmm) REVERT: J 21 MET cc_start: 0.5587 (mpm) cc_final: 0.4660 (pmm) REVERT: J 22 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5570 (pt) REVERT: J 69 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6750 (tpm-80) REVERT: K 21 MET cc_start: 0.5510 (mpm) cc_final: 0.4668 (pmm) REVERT: K 220 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6883 (tt) REVERT: L 21 MET cc_start: 0.5732 (mpm) cc_final: 0.4200 (tpp) outliers start: 56 outliers final: 13 residues processed: 228 average time/residue: 1.0129 time to fit residues: 265.6517 Evaluate side-chains 214 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 1.903 ------------------------------------------------------------------------------- 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 36 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 20 THR 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 25 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 253 PHE 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 20 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 69 ARG 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 179 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 156 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 115 optimal weight: 0.0970 chunk 112 optimal weight: 20.0000 chunk 85 optimal weight: 0.0870 chunk 114 optimal weight: 0.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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** ** D 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** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17220 Z= 0.134 Angle : 0.515 8.858 22944 Z= 0.251 Chirality : 0.039 0.122 2568 Planarity : 0.003 0.026 2712 Dihedral : 9.404 59.919 3072 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.70 % Allowed : 27.98 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.19), residues: 1908 helix: 2.37 (0.14), residues: 1296 sheet: 2.20 (0.37), residues: 120 loop : -0.50 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 79 HIS 0.002 0.001 HIS J 99 PHE 0.014 0.001 PHE A 33 TYR 0.013 0.001 TYR C 67 ARG 0.001 0.000 ARG H 77 *********************** 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 274 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 1.751 Fit side-chains REVERT: A 21 MET cc_start: 0.5758 (mpm) cc_final: 0.4693 (pmm) REVERT: A 22 ILE cc_start: 0.5776 (OUTLIER) cc_final: 0.5507 (pt) REVERT: A 220 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.6915 (tt) REVERT: B 21 MET cc_start: 0.5795 (mpm) cc_final: 0.4326 (tpp) REVERT: C 21 MET cc_start: 0.5433 (mpm) cc_final: 0.4576 (pmm) REVERT: C 22 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5530 (pt) REVERT: D 21 MET cc_start: 0.5614 (mpm) cc_final: 0.4723 (pmm) REVERT: D 22 ILE cc_start: 0.5725 (OUTLIER) cc_final: 0.5503 (pt) REVERT: D 220 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.6884 (tt) REVERT: E 21 MET cc_start: 0.5644 (mpm) cc_final: 0.4636 (pmm) REVERT: F 21 MET cc_start: 0.5692 (mpm) cc_final: 0.4848 (pmm) REVERT: F 22 ILE cc_start: 0.5733 (OUTLIER) cc_final: 0.5508 (pt) REVERT: F 69 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7343 (tpp-160) REVERT: G 21 MET cc_start: 0.5722 (mpm) cc_final: 0.4853 (pmm) REVERT: G 22 ILE cc_start: 0.5773 (OUTLIER) cc_final: 0.5533 (pt) REVERT: G 69 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7310 (tpp-160) REVERT: H 21 MET cc_start: 0.5655 (mpm) cc_final: 0.4694 (pmm) REVERT: H 22 ILE cc_start: 0.5770 (OUTLIER) cc_final: 0.5534 (pt) REVERT: H 220 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.6893 (tt) REVERT: I 21 MET cc_start: 0.5758 (mpm) cc_final: 0.4894 (pmm) REVERT: J 21 MET cc_start: 0.5458 (mpm) cc_final: 0.4583 (pmm) REVERT: J 22 ILE cc_start: 0.5781 (OUTLIER) cc_final: 0.5545 (pt) REVERT: J 69 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7388 (tpp-160) REVERT: K 21 MET cc_start: 0.5508 (mpm) cc_final: 0.4644 (pmm) REVERT: K 220 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.6889 (tt) REVERT: L 21 MET cc_start: 0.5761 (mpm) cc_final: 0.4239 (tpp) REVERT: L 274 HIS cc_start: 0.5230 (OUTLIER) cc_final: 0.4623 (m-70) outliers start: 48 outliers final: 11 residues processed: 260 average time/residue: 0.8940 time to fit residues: 270.6327 Evaluate side-chains 232 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 36 LEU Chi-restraints excluded: chain C residue 22 ILE 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 25 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 69 ARG 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 69 ARG 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 Chi-restraints excluded: chain L residue 274 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** ** D 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** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17220 Z= 0.302 Angle : 0.638 10.927 22944 Z= 0.312 Chirality : 0.044 0.149 2568 Planarity : 0.004 0.026 2712 Dihedral : 10.622 59.869 3072 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.87 % Allowed : 28.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 1908 helix: 1.85 (0.14), residues: 1296 sheet: 2.16 (0.38), residues: 120 loop : -0.53 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 79 HIS 0.003 0.001 HIS J 75 PHE 0.012 0.002 PHE A 33 TYR 0.026 0.002 TYR C 67 ARG 0.002 0.000 ARG I 246 *********************** 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 246 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 1.665 Fit side-chains REVERT: A 21 MET cc_start: 0.5686 (mpm) cc_final: 0.4760 (pmm) REVERT: B 21 MET cc_start: 0.5860 (mpm) cc_final: 0.4405 (tpp) REVERT: C 21 MET cc_start: 0.5501 (mpm) cc_final: 0.4592 (pmm) REVERT: C 22 ILE cc_start: 0.5826 (OUTLIER) cc_final: 0.5599 (pt) REVERT: D 21 MET cc_start: 0.5526 (mpm) cc_final: 0.4656 (pmm) REVERT: D 22 ILE cc_start: 0.5800 (OUTLIER) cc_final: 0.5578 (pt) REVERT: D 220 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.6984 (tt) REVERT: E 21 MET cc_start: 0.5653 (mpm) cc_final: 0.4450 (tpp) REVERT: F 21 MET cc_start: 0.5686 (mpm) cc_final: 0.4798 (pmm) REVERT: F 22 ILE cc_start: 0.5904 (OUTLIER) cc_final: 0.5702 (pt) REVERT: F 69 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6771 (tpm-80) REVERT: F 220 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6794 (tt) REVERT: G 21 MET cc_start: 0.5773 (mpm) cc_final: 0.4895 (pmm) REVERT: G 22 ILE cc_start: 0.5852 (OUTLIER) cc_final: 0.5602 (pt) REVERT: G 220 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6798 (tt) REVERT: H 21 MET cc_start: 0.5682 (mpm) cc_final: 0.4711 (pmm) REVERT: H 22 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5651 (pt) REVERT: H 220 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.6998 (tt) REVERT: I 21 MET cc_start: 0.5759 (mpm) cc_final: 0.4892 (pmm) REVERT: J 21 MET cc_start: 0.5443 (mpm) cc_final: 0.4615 (pmm) REVERT: J 22 ILE cc_start: 0.5809 (OUTLIER) cc_final: 0.5578 (pt) REVERT: K 21 MET cc_start: 0.5548 (mpm) cc_final: 0.4676 (pmm) REVERT: K 220 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.6944 (tt) REVERT: L 21 MET cc_start: 0.5783 (mpm) cc_final: 0.4241 (tpp) REVERT: L 274 HIS cc_start: 0.5281 (OUTLIER) cc_final: 0.4702 (m-70) outliers start: 51 outliers final: 11 residues processed: 239 average time/residue: 0.9781 time to fit residues: 269.0616 Evaluate side-chains 200 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 22 ILE 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 F residue 22 ILE Chi-restraints excluded: chain F residue 69 ARG 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 220 LEU 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 22 ILE 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 177 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** D 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** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17220 Z= 0.166 Angle : 0.535 8.972 22944 Z= 0.264 Chirality : 0.040 0.125 2568 Planarity : 0.004 0.026 2712 Dihedral : 9.588 59.720 3072 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.36 % Allowed : 29.22 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.19), residues: 1908 helix: 2.18 (0.14), residues: 1296 sheet: 2.31 (0.38), residues: 120 loop : -0.53 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 79 HIS 0.002 0.001 HIS B 99 PHE 0.013 0.001 PHE A 33 TYR 0.019 0.001 TYR C 67 ARG 0.001 0.000 ARG H 77 *********************** 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 230 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 1.666 Fit side-chains REVERT: A 21 MET cc_start: 0.5709 (mpm) cc_final: 0.4743 (pmm) REVERT: A 22 ILE cc_start: 0.5766 (OUTLIER) cc_final: 0.5532 (pt) REVERT: B 21 MET cc_start: 0.5802 (mpm) cc_final: 0.4324 (tpp) REVERT: C 21 MET cc_start: 0.5469 (mpm) cc_final: 0.4651 (pmm) REVERT: C 22 ILE cc_start: 0.5788 (OUTLIER) cc_final: 0.5561 (pt) REVERT: D 21 MET cc_start: 0.5483 (mpm) cc_final: 0.4652 (pmm) REVERT: D 22 ILE cc_start: 0.5755 (OUTLIER) cc_final: 0.5540 (pt) REVERT: D 220 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.6922 (tt) REVERT: E 21 MET cc_start: 0.5606 (mpm) cc_final: 0.4389 (tpp) REVERT: F 21 MET cc_start: 0.5774 (mpm) cc_final: 0.4850 (pmm) REVERT: F 22 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5609 (pt) REVERT: F 69 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6694 (tpm-80) REVERT: G 21 MET cc_start: 0.5662 (mpm) cc_final: 0.4784 (pmm) REVERT: G 22 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.5543 (pt) REVERT: G 69 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6750 (tpm-80) REVERT: H 21 MET cc_start: 0.5725 (mpm) cc_final: 0.4743 (pmm) REVERT: H 22 ILE cc_start: 0.5793 (OUTLIER) cc_final: 0.5576 (pt) REVERT: H 220 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.6981 (tt) REVERT: I 21 MET cc_start: 0.5741 (mpm) cc_final: 0.4879 (pmm) REVERT: J 21 MET cc_start: 0.5462 (mpm) cc_final: 0.4637 (pmm) REVERT: J 22 ILE cc_start: 0.5774 (OUTLIER) cc_final: 0.5540 (pt) REVERT: J 49 GLU cc_start: 0.8171 (pt0) cc_final: 0.7919 (pt0) REVERT: J 69 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6770 (tpm-80) REVERT: K 21 MET cc_start: 0.5580 (mpm) cc_final: 0.4740 (pmm) REVERT: K 220 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6944 (tt) REVERT: L 21 MET cc_start: 0.5661 (mpm) cc_final: 0.4172 (tpp) REVERT: L 274 HIS cc_start: 0.5249 (OUTLIER) cc_final: 0.4691 (m-70) outliers start: 42 outliers final: 15 residues processed: 223 average time/residue: 1.0625 time to fit residues: 272.9561 Evaluate side-chains 209 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 22 ILE 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 20 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 69 ARG 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 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 J residue 69 ARG 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 25 ILE 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 182 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** ** D 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17220 Z= 0.228 Angle : 0.580 9.120 22944 Z= 0.286 Chirality : 0.042 0.128 2568 Planarity : 0.004 0.026 2712 Dihedral : 9.868 59.983 3072 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.42 % Allowed : 29.17 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 1908 helix: 2.03 (0.14), residues: 1296 sheet: 2.25 (0.38), residues: 120 loop : -0.57 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.002 0.001 HIS B 99 PHE 0.013 0.001 PHE A 33 TYR 0.022 0.002 TYR G 67 ARG 0.002 0.000 ARG H 246 ********************** 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 220 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 1.700 Fit side-chains REVERT: A 21 MET cc_start: 0.5669 (mpm) cc_final: 0.4694 (pmm) REVERT: A 22 ILE cc_start: 0.5804 (OUTLIER) cc_final: 0.5577 (pt) REVERT: B 21 MET cc_start: 0.5845 (mpm) cc_final: 0.4390 (tpp) REVERT: C 21 MET cc_start: 0.5459 (mpm) cc_final: 0.4678 (pmm) REVERT: C 22 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5577 (pt) REVERT: D 21 MET cc_start: 0.5478 (mpm) cc_final: 0.4623 (pmm) REVERT: D 220 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6901 (tt) REVERT: E 21 MET cc_start: 0.5551 (mpm) cc_final: 0.4343 (tpp) REVERT: F 21 MET cc_start: 0.5791 (mpm) cc_final: 0.4856 (pmm) REVERT: F 69 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6711 (tpm-80) REVERT: G 21 MET cc_start: 0.5633 (mpm) cc_final: 0.4791 (pmm) REVERT: G 22 ILE cc_start: 0.5829 (OUTLIER) cc_final: 0.5598 (pt) REVERT: G 69 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6762 (tpm-80) REVERT: H 21 MET cc_start: 0.5668 (mpm) cc_final: 0.4708 (pmm) REVERT: H 22 ILE cc_start: 0.5851 (OUTLIER) cc_final: 0.5639 (pt) REVERT: H 220 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6947 (tt) REVERT: I 21 MET cc_start: 0.5759 (mpm) cc_final: 0.4880 (pmm) REVERT: J 21 MET cc_start: 0.5461 (mpm) cc_final: 0.4650 (pmm) REVERT: J 22 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5582 (pt) REVERT: J 69 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6758 (tpm-80) REVERT: K 21 MET cc_start: 0.5592 (mpm) cc_final: 0.4754 (pmm) REVERT: K 220 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.6926 (tt) REVERT: L 21 MET cc_start: 0.5661 (mpm) cc_final: 0.4278 (tpp) REVERT: L 274 HIS cc_start: 0.5351 (OUTLIER) cc_final: 0.4777 (m-70) outliers start: 43 outliers final: 18 residues processed: 211 average time/residue: 1.0620 time to fit residues: 256.1932 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 : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 36 LEU 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 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 57 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 69 ARG 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 20 THR Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 69 ARG 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 25 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.4980 chunk 46 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.0770 chunk 133 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** ** D 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** ** 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 = 0.4691 r_free = 0.4691 target = 0.248366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.214352 restraints weight = 15126.376| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 0.99 r_work: 0.4148 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3540 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: