Starting phenix.real_space_refine on Thu Mar 21 20:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8d_43035/03_2024/8v8d_43035_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8d_43035/03_2024/8v8d_43035.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8d_43035/03_2024/8v8d_43035_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8d_43035/03_2024/8v8d_43035_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8d_43035/03_2024/8v8d_43035_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8d_43035/03_2024/8v8d_43035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8d_43035/03_2024/8v8d_43035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8d_43035/03_2024/8v8d_43035_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8d_43035/03_2024/8v8d_43035_trim_updated.pdb" } resolution = 3.31 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= 0.006 sd= 0.021 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 S 115 5.16 5 Cl 10 4.86 5 C 10227 2.51 5 N 2498 2.21 5 O 2836 1.98 5 H 15085 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 258": "OE1" <-> "OE2" Residue "C GLU 1": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30774 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6060 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 6047 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 377, 6048 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 bond proxies already assigned to first conformer: 6118 Chain: "B" Number of atoms: 6036 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 376, 6023 Classifications: {'peptide': 376} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 376, 6024 Classifications: {'peptide': 376} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 355} Chain breaks: 1 bond proxies already assigned to first conformer: 6094 Chain: "C" Number of atoms: 6060 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 6047 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 377, 6048 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 bond proxies already assigned to first conformer: 6118 Chain: "D" Number of atoms: 6080 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 6068 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 bond proxies already assigned to first conformer: 6139 Chain: "E" Number of atoms: 6080 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 6068 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 bond proxies already assigned to first conformer: 6139 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 85 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 25.40, per 1000 atoms: 0.83 Number of scatterers: 30774 At special positions: 0 Unit cell: (89.925, 91.575, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 Cl 10 17.00 S 115 16.00 O 2836 8.00 N 2498 7.00 C 10227 6.00 H 15085 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.05 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.05 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.05 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 67 " " NAG A 602 " - " ASN A 23 " " NAG B 603 " - " ASN B 67 " " NAG B 604 " - " ASN B 23 " " NAG C 603 " - " ASN C 67 " " NAG C 604 " - " ASN C 23 " " NAG D 603 " - " ASN D 67 " " NAG D 604 " - " ASN D 23 " " NAG E 601 " - " ASN E 67 " " NAG E 602 " - " ASN E 23 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN B 110 " " NAG H 1 " - " ASN C 110 " " NAG I 1 " - " ASN D 110 " " NAG J 1 " - " ASN E 110 " Time building additional restraints: 22.74 Conformation dependent library (CDL) restraints added in 4.8 seconds 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 24 sheets defined 37.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.725A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 229 removed outlier: 4.383A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 238 through 259 removed outlier: 4.088A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 295 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 426 through 464 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 208 through 229 removed outlier: 4.731A pdb=" N ILE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Proline residue: B 217 - end of helix removed outlier: 4.458A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 238 through 259 removed outlier: 4.454A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 295 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 427 through 465 Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 229 removed outlier: 4.445A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.909A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 295 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 426 through 465 Processing helix chain 'C' and resid 470 through 476 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 229 removed outlier: 4.023A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 238 through 259 removed outlier: 4.291A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 295 Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 425 through 464 Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.750A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 230 removed outlier: 4.001A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 238 through 248 Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 269 through 295 Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 425 through 464 Processing helix chain 'E' and resid 470 through 477 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 6.011A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.880A pdb=" N ASP A 41 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= D, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.583A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 177 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU A 175 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.088A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= G, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= H, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= I, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.307A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 177 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B 175 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.074A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= L, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= M, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.511A pdb=" N PHE C 79 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.450A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 177 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU C 175 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.061A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 41 through 43 removed outlier: 3.508A pdb=" N ASP D 41 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= R, first strand: chain 'D' and resid 76 through 79 Processing sheet with id= S, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.229A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 177 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU D 175 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.055A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 41 through 43 removed outlier: 3.544A pdb=" N ASP E 41 " --> pdb=" O THR E 50 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= W, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.561A pdb=" N PHE E 79 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.599A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 177 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1998 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: 11.84 Time building geometry restraints manager: 23.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 4798 1.05 - 1.25: 12660 1.25 - 1.45: 4928 1.45 - 1.66: 8657 1.66 - 1.86: 180 Bond restraints: 31223 Sorted by residual: bond pdb=" C3 EPJ C 605 " pdb=" N1 EPJ C 605 " ideal model delta sigma weight residual 1.718 1.468 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C3 EPJ D 605 " pdb=" N1 EPJ D 605 " ideal model delta sigma weight residual 1.718 1.469 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C3 EPJ E 603 " pdb=" N1 EPJ E 603 " ideal model delta sigma weight residual 1.718 1.469 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C3 EPJ A 603 " pdb=" N1 EPJ A 603 " ideal model delta sigma weight residual 1.718 1.470 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C3 EPJ B 605 " pdb=" N1 EPJ B 605 " ideal model delta sigma weight residual 1.718 1.470 0.248 2.00e-02 2.50e+03 1.54e+02 ... (remaining 31218 not shown) Histogram of bond angle deviations from ideal: 94.90 - 110.22: 29053 110.22 - 125.55: 26540 125.55 - 140.87: 684 140.87 - 156.20: 0 156.20 - 171.53: 3 Bond angle restraints: 56280 Sorted by residual: angle pdb=" CA ARG A 425 " pdb=" N ARG A 425 " pdb=" H ARG A 425 " ideal model delta sigma weight residual 114.00 171.53 -57.53 3.00e+00 1.11e-01 3.68e+02 angle pdb=" CA PHE E 424 " pdb=" N PHE E 424 " pdb=" H PHE E 424 " ideal model delta sigma weight residual 114.00 161.64 -47.64 3.00e+00 1.11e-01 2.52e+02 angle pdb=" CA PHE D 424 " pdb=" N PHE D 424 " pdb=" H PHE D 424 " ideal model delta sigma weight residual 114.00 158.88 -44.88 3.00e+00 1.11e-01 2.24e+02 angle pdb=" N MET D 253 " pdb=" CA MET D 253 " pdb=" C MET D 253 " ideal model delta sigma weight residual 112.23 105.43 6.80 1.26e+00 6.30e-01 2.91e+01 angle pdb=" CA ASP B 137 " pdb=" CB ASP B 137 " pdb=" CG ASP B 137 " ideal model delta sigma weight residual 112.60 116.74 -4.14 1.00e+00 1.00e+00 1.72e+01 ... (remaining 56275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 13944 17.80 - 35.61: 815 35.61 - 53.41: 223 53.41 - 71.22: 68 71.22 - 89.02: 17 Dihedral angle restraints: 15067 sinusoidal: 8184 harmonic: 6883 Sorted by residual: dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual 180.00 -154.01 -25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 15064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2054 0.066 - 0.133: 374 0.133 - 0.199: 71 0.199 - 0.266: 6 0.266 - 0.332: 6 Chirality restraints: 2511 Sorted by residual: chirality pdb=" CB ILE C 178 " pdb=" CA ILE C 178 " pdb=" CG1 ILE C 178 " pdb=" CG2 ILE C 178 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C6 EPJ E 603 " pdb=" C1 EPJ E 603 " pdb=" C5 EPJ E 603 " pdb=" N1 EPJ E 603 " both_signs ideal model delta sigma weight residual False -2.80 -3.12 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C6 EPJ C 605 " pdb=" C1 EPJ C 605 " pdb=" C5 EPJ C 605 " pdb=" N1 EPJ C 605 " both_signs ideal model delta sigma weight residual False -2.80 -3.12 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 2508 not shown) Planarity restraints: 4483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 213 " -0.166 2.00e-02 2.50e+03 1.81e-01 4.93e+02 pdb=" CG ASN B 213 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 213 " 0.159 2.00e-02 2.50e+03 pdb=" ND2 ASN B 213 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 213 " 0.266 2.00e-02 2.50e+03 pdb="HD22 ASN B 213 " -0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 213 " -0.156 2.00e-02 2.50e+03 1.74e-01 4.52e+02 pdb=" CG ASN E 213 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN E 213 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN E 213 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN E 213 " 0.257 2.00e-02 2.50e+03 pdb="HD22 ASN E 213 " -0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 I34 C 601 " -0.041 2.00e-02 2.50e+03 1.04e-01 2.70e+02 pdb=" C04 I34 C 601 " -0.059 2.00e-02 2.50e+03 pdb=" C05 I34 C 601 " -0.029 2.00e-02 2.50e+03 pdb=" C08 I34 C 601 " 0.007 2.00e-02 2.50e+03 pdb=" C19 I34 C 601 " 0.012 2.00e-02 2.50e+03 pdb=" C20 I34 C 601 " -0.012 2.00e-02 2.50e+03 pdb=" N09 I34 C 601 " 0.156 2.00e-02 2.50e+03 pdb=" O02 I34 C 601 " 0.215 2.00e-02 2.50e+03 pdb=" O06 I34 C 601 " -0.111 2.00e-02 2.50e+03 pdb="CL1 I34 C 601 " -0.137 2.00e-02 2.50e+03 ... (remaining 4480 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1099 2.13 - 2.74: 53100 2.74 - 3.36: 84343 3.36 - 3.98: 118632 3.98 - 4.60: 177598 Nonbonded interactions: 434772 Sorted by model distance: nonbonded pdb=" HB VAL C 131 " pdb=" HE1 MET C 260 " model vdw 1.506 2.440 nonbonded pdb=" HZ3 LYS A 5 " pdb=" HH TYR A 71 " model vdw 1.509 2.100 nonbonded pdb="HD23 LEU B 246 " pdb="HD21 LEU C 224 " model vdw 1.524 2.440 nonbonded pdb=" HA GLU C 44 " pdb="HD12 ILE C 129 " model vdw 1.562 2.440 nonbonded pdb="HG23 THR B 308 " pdb="HD12 LEU B 312 " model vdw 1.595 2.440 ... (remaining 434767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 323 or resid 426 throug \ h 478)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 323 or resid 426 throug \ h 478)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 323 or resid 426 throug \ h 478)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 323 or resid 426 throug \ h 478)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 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: 2.390 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: 0.440 Extract box with map and model: 9.620 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 107.760 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 : 0.012 0.250 16138 Z= 0.759 Angle : 1.072 9.719 22003 Z= 0.534 Chirality : 0.056 0.332 2511 Planarity : 0.008 0.120 2697 Dihedral : 13.248 89.023 6085 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.12 % Allowed : 0.41 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.57 (0.18), residues: 1871 helix: -0.45 (0.18), residues: 718 sheet: -1.41 (0.22), residues: 434 loop : -1.19 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 315 HIS 0.013 0.002 HIS A 295 PHE 0.021 0.002 PHE E 229 TYR 0.023 0.002 TYR D 273 ARG 0.008 0.001 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 253 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 VAL cc_start: 0.9146 (t) cc_final: 0.8882 (t) REVERT: B 50 THR cc_start: 0.8140 (m) cc_final: 0.7846 (p) REVERT: B 253 MET cc_start: 0.6799 (mmm) cc_final: 0.6548 (mmm) REVERT: B 445 ASP cc_start: 0.7113 (m-30) cc_final: 0.6684 (m-30) REVERT: C 37 LEU cc_start: 0.7689 (mp) cc_final: 0.7149 (tp) REVERT: C 209 TYR cc_start: 0.8156 (t80) cc_final: 0.7766 (t80) REVERT: C 253 MET cc_start: 0.6889 (mmm) cc_final: 0.6578 (mtt) REVERT: C 448 CYS cc_start: 0.7580 (m) cc_final: 0.6710 (m) REVERT: E 118 LEU cc_start: 0.8165 (tt) cc_final: 0.7926 (tt) outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.5365 time to fit residues: 209.6526 Evaluate side-chains 207 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN B 213 ASN C 52 ASN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN D 272 GLN D 469 ASN E 3 GLN ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16138 Z= 0.193 Angle : 0.565 5.364 22003 Z= 0.293 Chirality : 0.041 0.177 2511 Planarity : 0.004 0.075 2697 Dihedral : 7.295 88.393 2513 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.94 % Allowed : 4.44 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.85 (0.18), residues: 1871 helix: 0.35 (0.19), residues: 712 sheet: -1.23 (0.22), residues: 412 loop : -0.92 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 307 HIS 0.004 0.001 HIS E 295 PHE 0.015 0.001 PHE D 455 TYR 0.012 0.001 TYR A 117 ARG 0.003 0.000 ARG E 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7705 (t0) cc_final: 0.7432 (t0) REVERT: B 450 MET cc_start: 0.6636 (ttp) cc_final: 0.6327 (ttp) REVERT: C 37 LEU cc_start: 0.7931 (mp) cc_final: 0.7131 (tp) REVERT: C 81 ASP cc_start: 0.7625 (t0) cc_final: 0.7391 (t0) REVERT: C 209 TYR cc_start: 0.8028 (t80) cc_final: 0.7704 (t80) REVERT: C 253 MET cc_start: 0.7008 (mmm) cc_final: 0.6566 (mtt) REVERT: C 445 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7023 (t0) REVERT: C 448 CYS cc_start: 0.7570 (m) cc_final: 0.6715 (m) REVERT: D 445 ASP cc_start: 0.6417 (m-30) cc_final: 0.6149 (m-30) REVERT: E 118 LEU cc_start: 0.8106 (tt) cc_final: 0.7798 (tt) outliers start: 16 outliers final: 10 residues processed: 214 average time/residue: 0.5998 time to fit residues: 193.5643 Evaluate side-chains 205 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 318 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 160 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16138 Z= 0.421 Angle : 0.625 5.572 22003 Z= 0.328 Chirality : 0.043 0.183 2511 Planarity : 0.005 0.059 2697 Dihedral : 6.869 82.479 2510 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.52 % Allowed : 5.32 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.77 (0.18), residues: 1871 helix: 0.41 (0.19), residues: 723 sheet: -1.36 (0.23), residues: 413 loop : -0.74 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 173 HIS 0.009 0.002 HIS E 296 PHE 0.019 0.002 PHE E 319 TYR 0.019 0.002 TYR D 209 ARG 0.007 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ILE cc_start: 0.8105 (mm) cc_final: 0.7593 (mm) REVERT: C 37 LEU cc_start: 0.8060 (mp) cc_final: 0.7334 (tp) REVERT: C 445 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7050 (t0) REVERT: C 448 CYS cc_start: 0.7584 (m) cc_final: 0.6817 (m) REVERT: C 472 GLU cc_start: 0.7562 (tt0) cc_final: 0.7353 (mm-30) REVERT: E 118 LEU cc_start: 0.8159 (tt) cc_final: 0.7822 (tt) REVERT: E 307 TRP cc_start: 0.5862 (m100) cc_final: 0.5650 (m100) outliers start: 26 outliers final: 22 residues processed: 219 average time/residue: 0.6453 time to fit residues: 212.7438 Evaluate side-chains 221 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 318 TRP Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS C 116 GLN ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16138 Z= 0.232 Angle : 0.523 4.347 22003 Z= 0.270 Chirality : 0.039 0.146 2511 Planarity : 0.004 0.052 2697 Dihedral : 6.366 82.332 2510 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.05 % Allowed : 6.55 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.45 (0.19), residues: 1871 helix: 0.84 (0.19), residues: 703 sheet: -1.34 (0.22), residues: 423 loop : -0.60 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 307 HIS 0.005 0.001 HIS E 295 PHE 0.015 0.001 PHE E 319 TYR 0.019 0.001 TYR D 209 ARG 0.003 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6884 (mmt) cc_final: 0.6201 (mmt) REVERT: C 37 LEU cc_start: 0.8018 (mp) cc_final: 0.7280 (tp) REVERT: C 116 GLN cc_start: 0.7657 (tt0) cc_final: 0.7374 (tt0) REVERT: C 448 CYS cc_start: 0.7553 (m) cc_final: 0.6788 (m) REVERT: E 40 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7315 (mtt) REVERT: E 118 LEU cc_start: 0.8096 (tt) cc_final: 0.7781 (tt) outliers start: 18 outliers final: 15 residues processed: 207 average time/residue: 0.5938 time to fit residues: 184.3740 Evaluate side-chains 210 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16138 Z= 0.219 Angle : 0.503 5.123 22003 Z= 0.259 Chirality : 0.039 0.202 2511 Planarity : 0.004 0.048 2697 Dihedral : 6.076 86.967 2510 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.40 % Allowed : 6.08 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.23 (0.19), residues: 1871 helix: 1.05 (0.19), residues: 705 sheet: -1.35 (0.22), residues: 437 loop : -0.40 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 307 HIS 0.005 0.001 HIS A 297 PHE 0.024 0.001 PHE E 319 TYR 0.018 0.001 TYR D 209 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6779 (mmt) cc_final: 0.6107 (mmt) REVERT: C 37 LEU cc_start: 0.8025 (mp) cc_final: 0.7286 (tp) REVERT: C 116 GLN cc_start: 0.7755 (tt0) cc_final: 0.7455 (tt0) REVERT: C 448 CYS cc_start: 0.7520 (m) cc_final: 0.6797 (m) REVERT: E 40 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7328 (mtt) REVERT: E 69 SER cc_start: 0.8824 (m) cc_final: 0.8577 (p) REVERT: E 118 LEU cc_start: 0.8077 (tt) cc_final: 0.7752 (tt) outliers start: 24 outliers final: 18 residues processed: 209 average time/residue: 0.5816 time to fit residues: 183.1662 Evaluate side-chains 215 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16138 Z= 0.384 Angle : 0.567 4.963 22003 Z= 0.297 Chirality : 0.041 0.169 2511 Planarity : 0.004 0.045 2697 Dihedral : 6.196 85.823 2510 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.46 % Allowed : 6.60 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.40 (0.19), residues: 1871 helix: 0.89 (0.19), residues: 701 sheet: -1.38 (0.22), residues: 435 loop : -0.50 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 54 HIS 0.007 0.001 HIS E 296 PHE 0.013 0.002 PHE A 136 TYR 0.019 0.002 TYR D 209 ARG 0.006 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7791 (ptt-90) cc_final: 0.7487 (ptt-90) REVERT: A 260 MET cc_start: 0.6924 (mmt) cc_final: 0.6208 (mmt) REVERT: C 37 LEU cc_start: 0.8055 (mp) cc_final: 0.7288 (tp) REVERT: C 445 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7088 (t0) REVERT: C 448 CYS cc_start: 0.7471 (m) cc_final: 0.6803 (m) REVERT: E 40 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7411 (mtt) REVERT: E 69 SER cc_start: 0.8842 (m) cc_final: 0.8636 (p) REVERT: E 118 LEU cc_start: 0.8105 (tt) cc_final: 0.7780 (tt) outliers start: 25 outliers final: 21 residues processed: 207 average time/residue: 0.6105 time to fit residues: 191.0300 Evaluate side-chains 218 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16138 Z= 0.259 Angle : 0.516 4.331 22003 Z= 0.267 Chirality : 0.039 0.161 2511 Planarity : 0.004 0.045 2697 Dihedral : 6.043 87.486 2510 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.34 % Allowed : 6.72 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.28 (0.19), residues: 1871 helix: 0.95 (0.19), residues: 710 sheet: -1.38 (0.22), residues: 434 loop : -0.37 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 437 HIS 0.005 0.001 HIS E 295 PHE 0.013 0.001 PHE A 134 TYR 0.018 0.001 TYR D 209 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7740 (ptt-90) cc_final: 0.7473 (ptt-90) REVERT: A 260 MET cc_start: 0.6859 (mmt) cc_final: 0.6154 (mmt) REVERT: A 474 VAL cc_start: 0.7801 (t) cc_final: 0.7431 (p) REVERT: C 37 LEU cc_start: 0.8018 (mp) cc_final: 0.7299 (tp) REVERT: C 448 CYS cc_start: 0.7437 (m) cc_final: 0.6755 (m) REVERT: E 40 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7362 (mtt) REVERT: E 69 SER cc_start: 0.8852 (m) cc_final: 0.8645 (p) REVERT: E 118 LEU cc_start: 0.8081 (tt) cc_final: 0.7778 (tt) outliers start: 23 outliers final: 20 residues processed: 206 average time/residue: 0.5916 time to fit residues: 183.1279 Evaluate side-chains 214 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 88 optimal weight: 0.0670 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 0.1980 chunk 162 optimal weight: 4.9990 overall best weight: 0.6536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16138 Z= 0.137 Angle : 0.470 4.276 22003 Z= 0.240 Chirality : 0.039 0.139 2511 Planarity : 0.004 0.045 2697 Dihedral : 5.844 87.778 2510 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.64 % Allowed : 7.60 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.13 (0.20), residues: 1871 helix: 1.27 (0.19), residues: 714 sheet: -1.20 (0.23), residues: 433 loop : -0.10 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 437 HIS 0.005 0.001 HIS E 295 PHE 0.015 0.001 PHE E 319 TYR 0.021 0.001 TYR D 209 ARG 0.002 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 200 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7661 (ptt-90) cc_final: 0.7385 (ptt-90) REVERT: A 260 MET cc_start: 0.6678 (mmt) cc_final: 0.5985 (mmt) REVERT: A 474 VAL cc_start: 0.7739 (t) cc_final: 0.7325 (p) REVERT: B 97 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6151 (mm-30) REVERT: C 37 LEU cc_start: 0.7986 (mp) cc_final: 0.7288 (tp) REVERT: C 445 ASP cc_start: 0.7377 (m-30) cc_final: 0.7044 (t70) REVERT: C 448 CYS cc_start: 0.7343 (m) cc_final: 0.6685 (m) REVERT: E 69 SER cc_start: 0.8856 (m) cc_final: 0.8637 (p) REVERT: E 228 VAL cc_start: 0.8333 (m) cc_final: 0.8099 (p) REVERT: E 304 MET cc_start: 0.6500 (mtp) cc_final: 0.6251 (mmm) outliers start: 11 outliers final: 10 residues processed: 206 average time/residue: 0.6212 time to fit residues: 193.8540 Evaluate side-chains 207 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 166 optimal weight: 0.0770 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 HIS ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16138 Z= 0.276 Angle : 0.508 4.985 22003 Z= 0.263 Chirality : 0.039 0.157 2511 Planarity : 0.004 0.043 2697 Dihedral : 5.889 88.682 2510 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.99 % Allowed : 7.31 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.04 (0.20), residues: 1871 helix: 1.20 (0.19), residues: 714 sheet: -1.23 (0.23), residues: 434 loop : -0.15 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 437 HIS 0.008 0.001 HIS C 295 PHE 0.012 0.001 PHE E 319 TYR 0.018 0.001 TYR D 209 ARG 0.005 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7738 (ptt-90) cc_final: 0.7492 (ptt-90) REVERT: A 280 ILE cc_start: 0.5737 (mm) cc_final: 0.5401 (mt) REVERT: A 474 VAL cc_start: 0.7768 (t) cc_final: 0.7360 (p) REVERT: C 37 LEU cc_start: 0.8010 (mp) cc_final: 0.7277 (tp) REVERT: C 448 CYS cc_start: 0.7374 (m) cc_final: 0.6722 (m) REVERT: E 40 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7331 (mtt) REVERT: E 69 SER cc_start: 0.8855 (m) cc_final: 0.8648 (p) REVERT: E 228 VAL cc_start: 0.8400 (m) cc_final: 0.8175 (p) REVERT: E 304 MET cc_start: 0.6606 (mtp) cc_final: 0.6371 (mmm) outliers start: 17 outliers final: 16 residues processed: 201 average time/residue: 0.6072 time to fit residues: 182.2517 Evaluate side-chains 210 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 0.0980 chunk 89 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16138 Z= 0.142 Angle : 0.468 4.661 22003 Z= 0.239 Chirality : 0.039 0.142 2511 Planarity : 0.003 0.044 2697 Dihedral : 5.756 88.822 2510 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.76 % Allowed : 7.66 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.26 (0.20), residues: 1871 helix: 1.42 (0.19), residues: 710 sheet: -1.12 (0.23), residues: 431 loop : -0.07 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 437 HIS 0.005 0.001 HIS E 295 PHE 0.015 0.001 PHE E 319 TYR 0.020 0.001 TYR D 209 ARG 0.002 0.000 ARG B 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3742 Ramachandran restraints generated. 1871 Oldfield, 0 Emsley, 1871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7690 (ptt-90) cc_final: 0.7441 (ptt-90) REVERT: A 260 MET cc_start: 0.6625 (mmt) cc_final: 0.5968 (mmt) REVERT: A 280 ILE cc_start: 0.5751 (mm) cc_final: 0.5404 (mt) REVERT: A 297 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7647 (t-170) REVERT: A 474 VAL cc_start: 0.7735 (t) cc_final: 0.7320 (p) REVERT: B 97 GLU cc_start: 0.6526 (mt-10) cc_final: 0.6147 (mm-30) REVERT: C 37 LEU cc_start: 0.7967 (mp) cc_final: 0.7255 (tp) REVERT: C 448 CYS cc_start: 0.7330 (m) cc_final: 0.6691 (m) REVERT: D 307 TRP cc_start: 0.6811 (m100) cc_final: 0.6588 (m100) REVERT: E 69 SER cc_start: 0.8846 (m) cc_final: 0.8638 (p) REVERT: E 228 VAL cc_start: 0.8360 (m) cc_final: 0.8150 (p) REVERT: E 304 MET cc_start: 0.6517 (mtp) cc_final: 0.6290 (mmm) outliers start: 13 outliers final: 11 residues processed: 207 average time/residue: 0.6095 time to fit residues: 189.2999 Evaluate side-chains 207 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 455 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.123831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.108962 restraints weight = 99178.789| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.36 r_work: 0.3537 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16138 Z= 0.201 Angle : 0.483 4.627 22003 Z= 0.248 Chirality : 0.038 0.146 2511 Planarity : 0.004 0.043 2697 Dihedral : 5.665 89.219 2510 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.88 % Allowed : 7.66 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.26 (0.20), residues: 1871 helix: 1.41 (0.19), residues: 710 sheet: -1.08 (0.23), residues: 429 loop : -0.09 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 437 HIS 0.004 0.001 HIS E 295 PHE 0.013 0.001 PHE E 319 TYR 0.018 0.001 TYR D 209 ARG 0.004 0.000 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6419.18 seconds wall clock time: 114 minutes 2.62 seconds (6842.62 seconds total)