Starting phenix.real_space_refine on Wed Feb 14 17:26:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/02_2024/7wut_32841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/02_2024/7wut_32841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/02_2024/7wut_32841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/02_2024/7wut_32841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/02_2024/7wut_32841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/02_2024/7wut_32841.pdb" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 128 atoms to isotropic. 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 76 5.16 5 C 6100 2.51 5 N 1728 2.21 5 O 1828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 23": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C ASP 176": "OD1" <-> "OD2" Residue "C ASP 197": "OD1" <-> "OD2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D ASP 197": "OD1" <-> "OD2" Residue "D PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 299": "NH1" <-> "NH2" Residue "D TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9732 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2433 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "B" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2433 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2433 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "D" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2433 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 76 Time building chain proxies: 5.16, per 1000 atoms: 0.53 Number of scatterers: 9732 At special positions: 0 Unit cell: (114.84, 85.8, 85.8, 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 76 16.00 O 1828 8.00 N 1728 7.00 C 6100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 223 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 312 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 316 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 143 " distance=2.03 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 223 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 329 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 312 " distance=2.03 Simple disulfide: pdb=" SG CYS D 313 " - pdb=" SG CYS D 316 " distance=2.03 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 Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 17.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 38 through 51 removed outlier: 4.326A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 78 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'B' and resid 38 through 51 removed outlier: 4.313A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 79 Proline residue: B 73 - end of helix removed outlier: 3.596A pdb=" N LEU B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'C' and resid 38 through 51 removed outlier: 4.290A pdb=" N LEU C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 79 Proline residue: C 73 - end of helix removed outlier: 3.587A pdb=" N LEU C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 83 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'D' and resid 38 through 51 removed outlier: 4.288A pdb=" N LEU D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 79 Proline residue: D 73 - end of helix removed outlier: 3.588A pdb=" N LEU D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 83 Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 252 through 256 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.812A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.041A pdb=" N ASP A 276 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 324 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE A 212 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ALA A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 216 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 192 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 216 " --> pdb=" O TRP C 201 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA C 205 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE C 212 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N GLU C 213 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE C 277 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 324 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP C 276 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287 removed outlier: 6.973A pdb=" N VAL A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57 removed outlier: 6.775A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AA7, first strand: chain 'B' and resid 329 through 331 removed outlier: 4.046A pdb=" N ASP B 276 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 324 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE B 212 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA B 205 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 216 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG D 192 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 216 " --> pdb=" O TRP D 201 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA D 205 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ILE D 212 " --> pdb=" O ALA D 205 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLU D 213 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE D 277 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 324 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP D 276 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 286 through 287 removed outlier: 6.972A pdb=" N VAL B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 57 removed outlier: 6.765A pdb=" N GLY C 56 " --> pdb=" O ALA C 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AB2, first strand: chain 'C' and resid 286 through 287 removed outlier: 6.984A pdb=" N VAL C 286 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 56 through 57 removed outlier: 6.770A pdb=" N GLY D 56 " --> pdb=" O ALA D 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AB5, first strand: chain 'D' and resid 286 through 287 removed outlier: 6.977A pdb=" N VAL D 286 " --> pdb=" O CYS D 313 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3226 1.34 - 1.46: 2163 1.46 - 1.58: 4467 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 9964 Sorted by residual: bond pdb=" N GLN C 31 " pdb=" CA GLN C 31 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.11e+00 bond pdb=" N GLN B 31 " pdb=" CA GLN B 31 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.08e+00 bond pdb=" N GLN D 31 " pdb=" CA GLN D 31 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.06e+00 bond pdb=" N GLN A 31 " pdb=" CA GLN A 31 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.05e+00 bond pdb=" N GLU A 156 " pdb=" CA GLU A 156 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 1.99e+00 ... (remaining 9959 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.22: 325 106.22 - 113.19: 5423 113.19 - 120.16: 3280 120.16 - 127.14: 4282 127.14 - 134.11: 210 Bond angle restraints: 13520 Sorted by residual: angle pdb=" C VAL B 155 " pdb=" N GLU B 156 " pdb=" CA GLU B 156 " ideal model delta sigma weight residual 121.70 131.51 -9.81 1.80e+00 3.09e-01 2.97e+01 angle pdb=" C VAL D 155 " pdb=" N GLU D 156 " pdb=" CA GLU D 156 " ideal model delta sigma weight residual 121.70 131.50 -9.80 1.80e+00 3.09e-01 2.97e+01 angle pdb=" C VAL C 155 " pdb=" N GLU C 156 " pdb=" CA GLU C 156 " ideal model delta sigma weight residual 121.70 131.48 -9.78 1.80e+00 3.09e-01 2.95e+01 angle pdb=" C GLU A 30 " pdb=" N GLN A 31 " pdb=" CA GLN A 31 " ideal model delta sigma weight residual 121.70 131.45 -9.75 1.80e+00 3.09e-01 2.94e+01 angle pdb=" C GLU C 30 " pdb=" N GLN C 31 " pdb=" CA GLN C 31 " ideal model delta sigma weight residual 121.70 131.44 -9.74 1.80e+00 3.09e-01 2.93e+01 ... (remaining 13515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 5050 15.62 - 31.23: 678 31.23 - 46.85: 199 46.85 - 62.47: 73 62.47 - 78.08: 16 Dihedral angle restraints: 6016 sinusoidal: 2392 harmonic: 3624 Sorted by residual: dihedral pdb=" CB CYS D 313 " pdb=" SG CYS D 313 " pdb=" SG CYS D 316 " pdb=" CB CYS D 316 " ideal model delta sinusoidal sigma weight residual 93.00 38.82 54.18 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 316 " pdb=" CB CYS B 316 " ideal model delta sinusoidal sigma weight residual 93.00 38.89 54.11 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 316 " pdb=" CB CYS A 316 " ideal model delta sinusoidal sigma weight residual 93.00 39.05 53.95 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 6013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 959 0.035 - 0.070: 339 0.070 - 0.105: 119 0.105 - 0.141: 54 0.141 - 0.176: 9 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CA THR C 72 " pdb=" N THR C 72 " pdb=" C THR C 72 " pdb=" CB THR C 72 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA THR B 72 " pdb=" N THR B 72 " pdb=" C THR B 72 " pdb=" CB THR B 72 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA THR D 72 " pdb=" N THR D 72 " pdb=" C THR D 72 " pdb=" CB THR D 72 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 1477 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 72 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO D 73 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 73 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 73 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 72 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO C 73 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 73 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 73 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 72 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 73 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.020 5.00e-02 4.00e+02 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 333 2.69 - 3.24: 9875 3.24 - 3.80: 15637 3.80 - 4.35: 19508 4.35 - 4.90: 31111 Nonbonded interactions: 76464 Sorted by model distance: nonbonded pdb=" OD2 ASP B 23 " pdb=" OG SER B 185 " model vdw 2.139 2.440 nonbonded pdb=" OD2 ASP A 23 " pdb=" OG SER A 185 " model vdw 2.151 2.440 nonbonded pdb=" OD2 ASP C 23 " pdb=" OG SER C 185 " model vdw 2.160 2.440 nonbonded pdb=" OD2 ASP D 23 " pdb=" OG SER D 185 " model vdw 2.190 2.440 nonbonded pdb=" OG1 THR B 300 " pdb=" O CYS B 329 " model vdw 2.267 2.440 ... (remaining 76459 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 1.440 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.150 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9964 Z= 0.193 Angle : 0.833 10.516 13520 Z= 0.418 Chirality : 0.046 0.176 1480 Planarity : 0.004 0.036 1740 Dihedral : 16.782 78.083 3612 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.30 % Favored : 86.38 % Rotamer: Outliers : 0.20 % Allowed : 32.13 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -1.82 (0.24), residues: 1248 helix: 0.09 (0.48), residues: 128 sheet: 0.00 (0.77), residues: 60 loop : -1.61 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 225 HIS 0.004 0.001 HIS A 254 PHE 0.005 0.001 PHE A 217 TYR 0.006 0.001 TYR D 256 ARG 0.006 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.219 Fit side-chains REVERT: A 136 ASP cc_start: 0.8745 (t0) cc_final: 0.7851 (t70) REVERT: A 241 MET cc_start: 0.8010 (mmm) cc_final: 0.7703 (mtt) REVERT: B 86 LEU cc_start: 0.8778 (pp) cc_final: 0.8501 (tp) REVERT: C 86 LEU cc_start: 0.8739 (pp) cc_final: 0.8499 (tp) REVERT: D 86 LEU cc_start: 0.8729 (pp) cc_final: 0.8488 (tp) outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.1699 time to fit residues: 20.0923 Evaluate side-chains 73 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 40.0000 chunk 112 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 9964 Z= 0.474 Angle : 0.917 10.235 13520 Z= 0.476 Chirality : 0.048 0.188 1480 Planarity : 0.005 0.034 1740 Dihedral : 5.919 32.766 1342 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 16.83 % Favored : 82.85 % Rotamer: Outliers : 7.71 % Allowed : 28.91 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -2.14 (0.24), residues: 1248 helix: -0.09 (0.45), residues: 144 sheet: -0.81 (0.58), residues: 92 loop : -1.85 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 225 HIS 0.006 0.002 HIS C 254 PHE 0.015 0.002 PHE C 217 TYR 0.008 0.001 TYR A 323 ARG 0.007 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 62 time to evaluate : 1.177 Fit side-chains REVERT: A 42 LEU cc_start: 0.9484 (tt) cc_final: 0.8972 (mp) REVERT: A 190 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8859 (p0) REVERT: A 195 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8081 (m90) REVERT: A 227 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8860 (mmtt) REVERT: A 242 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 275 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8229 (mmp) REVERT: B 42 LEU cc_start: 0.9486 (tt) cc_final: 0.9000 (mp) REVERT: B 190 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8840 (p0) REVERT: B 195 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.8079 (m90) REVERT: B 227 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8873 (mmtt) REVERT: B 242 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8939 (mm) REVERT: B 275 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8194 (mmp) REVERT: C 42 LEU cc_start: 0.9478 (tt) cc_final: 0.8973 (mp) REVERT: C 190 ASP cc_start: 0.9191 (OUTLIER) cc_final: 0.8861 (p0) REVERT: C 195 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.8102 (m90) REVERT: C 227 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8991 (mmmt) REVERT: C 242 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8956 (mm) REVERT: C 275 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8197 (mmp) REVERT: D 42 LEU cc_start: 0.9481 (tt) cc_final: 0.8980 (mp) REVERT: D 190 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8846 (p0) REVERT: D 195 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.8079 (m90) REVERT: D 227 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8868 (mmmt) REVERT: D 275 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8212 (mmp) outliers start: 79 outliers final: 29 residues processed: 130 average time/residue: 0.1861 time to fit residues: 35.7314 Evaluate side-chains 115 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 67 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 232 TRP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 232 TRP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 232 TRP Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9964 Z= 0.338 Angle : 0.847 10.079 13520 Z= 0.440 Chirality : 0.047 0.171 1480 Planarity : 0.004 0.035 1740 Dihedral : 5.718 22.727 1340 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 16.19 % Favored : 83.49 % Rotamer: Outliers : 6.15 % Allowed : 31.15 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -2.11 (0.24), residues: 1248 helix: 0.16 (0.47), residues: 144 sheet: -0.95 (0.58), residues: 100 loop : -1.86 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 225 HIS 0.005 0.001 HIS A 254 PHE 0.009 0.002 PHE D 217 TYR 0.010 0.001 TYR A 323 ARG 0.004 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 75 time to evaluate : 1.160 Fit side-chains REVERT: A 190 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8777 (p0) REVERT: A 195 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8123 (m90) REVERT: A 227 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8849 (mmtt) REVERT: A 275 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8076 (mmp) REVERT: A 323 TYR cc_start: 0.7349 (m-80) cc_final: 0.6666 (m-80) REVERT: B 190 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8758 (p0) REVERT: B 195 HIS cc_start: 0.8514 (OUTLIER) cc_final: 0.8127 (m90) REVERT: B 227 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8884 (mmmt) REVERT: B 241 MET cc_start: 0.8826 (mmm) cc_final: 0.8253 (mtt) REVERT: B 242 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8981 (mm) REVERT: B 275 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8066 (mmp) REVERT: B 323 TYR cc_start: 0.7324 (m-80) cc_final: 0.6659 (m-80) REVERT: B 333 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7988 (ptp) REVERT: C 42 LEU cc_start: 0.9479 (tt) cc_final: 0.8937 (mp) REVERT: C 190 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8786 (p0) REVERT: C 195 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.8143 (m90) REVERT: C 242 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8972 (mm) REVERT: C 275 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7997 (mmp) REVERT: C 323 TYR cc_start: 0.7350 (m-80) cc_final: 0.6487 (m-80) REVERT: D 190 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8772 (p0) REVERT: D 195 HIS cc_start: 0.8514 (OUTLIER) cc_final: 0.8126 (m90) REVERT: D 227 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8833 (mmtt) REVERT: D 242 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8932 (mm) REVERT: D 275 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8003 (mmp) REVERT: D 323 TYR cc_start: 0.7371 (m-80) cc_final: 0.6495 (m-80) REVERT: D 333 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7850 (ptp) outliers start: 63 outliers final: 24 residues processed: 126 average time/residue: 0.1634 time to fit residues: 31.6433 Evaluate side-chains 115 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 71 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 232 TRP Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 232 TRP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 232 TRP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9964 Z= 0.239 Angle : 0.825 10.705 13520 Z= 0.426 Chirality : 0.046 0.174 1480 Planarity : 0.004 0.032 1740 Dihedral : 5.396 22.589 1340 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.98 % Favored : 84.70 % Rotamer: Outliers : 4.20 % Allowed : 31.93 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -1.98 (0.24), residues: 1248 helix: 0.31 (0.49), residues: 144 sheet: -1.10 (0.58), residues: 100 loop : -1.74 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 225 HIS 0.003 0.001 HIS B 195 PHE 0.010 0.001 PHE B 217 TYR 0.012 0.001 TYR A 323 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 76 time to evaluate : 1.205 Fit side-chains REVERT: A 190 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8650 (p0) REVERT: A 242 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8887 (mm) REVERT: A 323 TYR cc_start: 0.7446 (m-80) cc_final: 0.6670 (m-80) REVERT: B 190 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8650 (p0) REVERT: B 227 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8839 (mmmt) REVERT: B 241 MET cc_start: 0.8753 (mmm) cc_final: 0.8230 (mtt) REVERT: B 323 TYR cc_start: 0.7476 (m-80) cc_final: 0.6686 (m-80) REVERT: C 190 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8666 (p0) REVERT: C 227 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8982 (mmmt) REVERT: C 323 TYR cc_start: 0.7449 (m-80) cc_final: 0.6678 (m-80) REVERT: D 190 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8658 (p0) REVERT: D 242 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8915 (mm) REVERT: D 323 TYR cc_start: 0.7510 (m-80) cc_final: 0.6694 (m-80) outliers start: 43 outliers final: 25 residues processed: 113 average time/residue: 0.1700 time to fit residues: 29.5805 Evaluate side-chains 103 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 70 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 232 TRP Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 232 TRP Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 232 TRP Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 0.1980 chunk 102 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 overall best weight: 5.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9964 Z= 0.371 Angle : 0.868 10.041 13520 Z= 0.450 Chirality : 0.047 0.166 1480 Planarity : 0.004 0.032 1740 Dihedral : 5.681 21.867 1340 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 16.03 % Favored : 83.65 % Rotamer: Outliers : 6.45 % Allowed : 29.98 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -2.06 (0.24), residues: 1248 helix: 0.22 (0.48), residues: 144 sheet: -1.10 (0.48), residues: 124 loop : -1.81 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 225 HIS 0.007 0.002 HIS A 195 PHE 0.011 0.002 PHE C 217 TYR 0.009 0.001 TYR A 323 ARG 0.004 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 70 time to evaluate : 1.170 Fit side-chains REVERT: A 190 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8756 (p0) REVERT: A 242 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8972 (mm) REVERT: A 275 MET cc_start: 0.8616 (mmp) cc_final: 0.8277 (mmp) REVERT: A 323 TYR cc_start: 0.7378 (m-80) cc_final: 0.6869 (m-80) REVERT: B 190 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8744 (p0) REVERT: B 227 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8831 (mmtt) REVERT: B 242 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8971 (mm) REVERT: B 275 MET cc_start: 0.8604 (mmp) cc_final: 0.8260 (mmp) REVERT: C 26 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7330 (t-90) REVERT: C 190 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8775 (p0) REVERT: C 227 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8999 (mmmt) REVERT: C 241 MET cc_start: 0.8957 (mmm) cc_final: 0.8197 (mtt) REVERT: C 242 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8983 (mm) REVERT: C 275 MET cc_start: 0.8602 (mmp) cc_final: 0.8244 (mmp) REVERT: C 323 TYR cc_start: 0.7416 (m-80) cc_final: 0.6891 (m-80) REVERT: D 190 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8770 (p0) REVERT: D 227 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8978 (mmmm) REVERT: D 242 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8988 (mm) REVERT: D 275 MET cc_start: 0.8598 (mmp) cc_final: 0.8257 (mmp) REVERT: D 323 TYR cc_start: 0.7433 (m-80) cc_final: 0.6906 (m-80) REVERT: D 333 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7740 (ptp) outliers start: 66 outliers final: 41 residues processed: 124 average time/residue: 0.1797 time to fit residues: 34.2152 Evaluate side-chains 124 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 70 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 232 TRP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 232 TRP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 232 TRP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 0.0010 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9964 Z= 0.297 Angle : 0.833 10.319 13520 Z= 0.431 Chirality : 0.046 0.168 1480 Planarity : 0.004 0.033 1740 Dihedral : 5.560 22.272 1340 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.74 % Favored : 84.94 % Rotamer: Outliers : 5.57 % Allowed : 30.76 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -2.01 (0.24), residues: 1248 helix: 0.28 (0.47), residues: 144 sheet: -1.09 (0.48), residues: 124 loop : -1.77 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 225 HIS 0.004 0.001 HIS D 254 PHE 0.012 0.002 PHE D 217 TYR 0.010 0.001 TYR C 323 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 76 time to evaluate : 1.132 Fit side-chains REVERT: A 190 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8736 (p0) REVERT: A 227 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8813 (mmmm) REVERT: A 242 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8996 (mm) REVERT: A 275 MET cc_start: 0.8602 (mmp) cc_final: 0.8313 (mmp) REVERT: A 323 TYR cc_start: 0.7420 (m-80) cc_final: 0.7006 (m-80) REVERT: B 190 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8726 (p0) REVERT: B 242 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9001 (mm) REVERT: B 275 MET cc_start: 0.8639 (mmp) cc_final: 0.8320 (mmt) REVERT: C 190 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8696 (p0) REVERT: C 227 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8997 (mmmt) REVERT: C 241 MET cc_start: 0.8952 (mmm) cc_final: 0.8130 (mtt) REVERT: C 242 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8966 (mm) REVERT: C 275 MET cc_start: 0.8591 (mmp) cc_final: 0.8244 (mmp) REVERT: C 323 TYR cc_start: 0.7421 (m-80) cc_final: 0.6958 (m-80) REVERT: D 190 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8730 (p0) REVERT: D 242 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.8974 (mm) REVERT: D 275 MET cc_start: 0.8589 (mmp) cc_final: 0.8258 (mmp) REVERT: D 323 TYR cc_start: 0.7444 (m-80) cc_final: 0.6971 (m-80) outliers start: 57 outliers final: 41 residues processed: 124 average time/residue: 0.1678 time to fit residues: 31.8511 Evaluate side-chains 124 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 73 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 232 TRP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 232 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 232 TRP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9964 Z= 0.273 Angle : 0.832 10.287 13520 Z= 0.427 Chirality : 0.046 0.168 1480 Planarity : 0.004 0.031 1740 Dihedral : 5.474 22.277 1340 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.98 % Favored : 84.70 % Rotamer: Outliers : 6.05 % Allowed : 30.37 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -1.98 (0.25), residues: 1248 helix: 0.30 (0.47), residues: 144 sheet: -1.08 (0.49), residues: 124 loop : -1.75 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 225 HIS 0.003 0.001 HIS B 254 PHE 0.012 0.002 PHE D 217 TYR 0.010 0.001 TYR D 323 ARG 0.003 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 75 time to evaluate : 1.189 Fit side-chains REVERT: A 26 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7455 (t-90) REVERT: A 190 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8723 (p0) REVERT: A 225 TRP cc_start: 0.8018 (t-100) cc_final: 0.7768 (t-100) REVERT: A 227 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8808 (mmmm) REVERT: A 241 MET cc_start: 0.8715 (mtt) cc_final: 0.8038 (mtt) REVERT: A 242 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8990 (mm) REVERT: A 323 TYR cc_start: 0.7160 (m-80) cc_final: 0.6755 (m-80) REVERT: B 190 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8709 (p0) REVERT: B 227 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8798 (mmmm) REVERT: B 242 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.8999 (mm) REVERT: B 275 MET cc_start: 0.8643 (mmp) cc_final: 0.8345 (mmt) REVERT: C 26 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.7395 (t-90) REVERT: C 190 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8740 (p0) REVERT: C 227 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8977 (mmmt) REVERT: C 242 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9003 (mm) REVERT: C 323 TYR cc_start: 0.7410 (m-80) cc_final: 0.6998 (m-80) REVERT: D 190 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8713 (p0) REVERT: D 227 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8836 (mmmt) REVERT: D 241 MET cc_start: 0.8723 (mtt) cc_final: 0.8028 (mtt) REVERT: D 242 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8968 (mm) REVERT: D 323 TYR cc_start: 0.7431 (m-80) cc_final: 0.6974 (m-80) outliers start: 62 outliers final: 42 residues processed: 127 average time/residue: 0.1844 time to fit residues: 34.8270 Evaluate side-chains 132 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 76 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 232 TRP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 232 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 232 TRP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 75 optimal weight: 0.0870 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 108 optimal weight: 0.0060 overall best weight: 4.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9964 Z= 0.321 Angle : 0.860 10.221 13520 Z= 0.440 Chirality : 0.047 0.168 1480 Planarity : 0.004 0.031 1740 Dihedral : 5.564 22.043 1340 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 15.87 % Favored : 83.81 % Rotamer: Outliers : 6.54 % Allowed : 29.79 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -2.03 (0.24), residues: 1248 helix: 0.33 (0.47), residues: 144 sheet: -1.13 (0.48), residues: 124 loop : -1.79 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 225 HIS 0.004 0.001 HIS C 254 PHE 0.011 0.002 PHE B 217 TYR 0.009 0.001 TYR D 323 ARG 0.003 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 80 time to evaluate : 1.207 Fit side-chains REVERT: A 26 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7442 (t-90) REVERT: A 190 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8740 (p0) REVERT: A 195 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8234 (m170) REVERT: A 227 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8857 (mmtt) REVERT: A 241 MET cc_start: 0.8735 (mtt) cc_final: 0.8062 (mtt) REVERT: A 242 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.8975 (mm) REVERT: B 26 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7487 (t-90) REVERT: B 190 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8726 (p0) REVERT: B 195 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.8222 (m170) REVERT: B 227 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8807 (mmmm) REVERT: B 242 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.8964 (mm) REVERT: B 275 MET cc_start: 0.8675 (mmp) cc_final: 0.8380 (mmt) REVERT: C 26 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7347 (t-90) REVERT: C 190 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8759 (p0) REVERT: C 227 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8926 (mmmm) REVERT: C 242 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8962 (mm) REVERT: D 190 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8730 (p0) REVERT: D 227 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8805 (mmmm) REVERT: D 241 MET cc_start: 0.8768 (mtt) cc_final: 0.8452 (mtt) REVERT: D 242 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8975 (mm) REVERT: D 275 MET cc_start: 0.8608 (mmp) cc_final: 0.8175 (mmt) outliers start: 67 outliers final: 46 residues processed: 138 average time/residue: 0.1862 time to fit residues: 38.7420 Evaluate side-chains 138 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 75 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 232 TRP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 232 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 232 TRP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 77 HIS ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9964 Z= 0.252 Angle : 0.844 10.256 13520 Z= 0.427 Chirality : 0.047 0.171 1480 Planarity : 0.003 0.031 1740 Dihedral : 5.396 22.431 1340 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.74 % Favored : 84.94 % Rotamer: Outliers : 5.18 % Allowed : 30.76 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -1.97 (0.25), residues: 1248 helix: 0.27 (0.48), residues: 144 sheet: -1.09 (0.49), residues: 124 loop : -1.73 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 225 HIS 0.004 0.001 HIS D 77 PHE 0.011 0.002 PHE B 217 TYR 0.012 0.001 TYR A 323 ARG 0.003 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 77 time to evaluate : 1.269 Fit side-chains REVERT: A 26 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7444 (t-90) REVERT: A 190 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8719 (p0) REVERT: A 275 MET cc_start: 0.8505 (mmp) cc_final: 0.8302 (mmp) REVERT: B 190 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8729 (p0) REVERT: B 242 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8983 (mm) REVERT: B 275 MET cc_start: 0.8634 (mmp) cc_final: 0.8324 (mmt) REVERT: C 26 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7315 (t-90) REVERT: C 190 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8753 (p0) REVERT: C 227 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8990 (mmmt) REVERT: C 242 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8965 (mm) REVERT: C 275 MET cc_start: 0.8603 (mmp) cc_final: 0.8290 (mmt) REVERT: D 190 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8712 (p0) REVERT: D 225 TRP cc_start: 0.8064 (t-100) cc_final: 0.7746 (t-100) REVERT: D 227 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8823 (mmmt) REVERT: D 241 MET cc_start: 0.8801 (mtt) cc_final: 0.8565 (mtt) REVERT: D 242 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8956 (mm) REVERT: D 275 MET cc_start: 0.8595 (mmp) cc_final: 0.8270 (mmt) outliers start: 53 outliers final: 40 residues processed: 122 average time/residue: 0.1647 time to fit residues: 31.3312 Evaluate side-chains 128 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 77 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 232 TRP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 232 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 232 TRP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9964 Z= 0.289 Angle : 0.859 10.302 13520 Z= 0.435 Chirality : 0.047 0.169 1480 Planarity : 0.004 0.031 1740 Dihedral : 5.438 22.224 1340 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.32 % Allowed : 15.71 % Favored : 83.97 % Rotamer: Outliers : 5.66 % Allowed : 30.37 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -1.98 (0.25), residues: 1248 helix: 0.27 (0.48), residues: 144 sheet: -0.97 (0.59), residues: 100 loop : -1.75 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 225 HIS 0.004 0.001 HIS D 77 PHE 0.011 0.002 PHE B 217 TYR 0.012 0.001 TYR C 323 ARG 0.003 0.000 ARG D 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 76 time to evaluate : 1.191 Fit side-chains REVERT: A 26 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7432 (t-90) REVERT: A 190 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8731 (p0) REVERT: A 242 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8959 (mm) REVERT: B 26 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7438 (t-90) REVERT: B 190 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8720 (p0) REVERT: B 242 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8955 (mm) REVERT: B 275 MET cc_start: 0.8666 (mmp) cc_final: 0.8371 (mmt) REVERT: C 26 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.7372 (t-90) REVERT: C 190 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8761 (p0) REVERT: C 227 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8951 (mmmm) REVERT: C 242 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8973 (mm) REVERT: D 190 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8725 (p0) REVERT: D 227 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8873 (mmmm) REVERT: D 241 MET cc_start: 0.8777 (mtt) cc_final: 0.8456 (mtt) REVERT: D 242 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8966 (mm) outliers start: 58 outliers final: 45 residues processed: 125 average time/residue: 0.1703 time to fit residues: 32.9979 Evaluate side-chains 133 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 75 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 232 TRP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 232 TRP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 329 CYS Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 26 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 113 TYR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 232 TRP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 232 TRP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 101 optimal weight: 0.0040 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 2.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.112550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.076306 restraints weight = 33497.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.079248 restraints weight = 18119.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.081230 restraints weight = 12598.645| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9964 Z= 0.223 Angle : 0.837 10.508 13520 Z= 0.420 Chirality : 0.047 0.172 1480 Planarity : 0.004 0.030 1740 Dihedral : 5.258 22.736 1340 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.34 % Favored : 85.34 % Rotamer: Outliers : 4.79 % Allowed : 31.45 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 5.03 % 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: -1.92 (0.25), residues: 1248 helix: 0.26 (0.47), residues: 144 sheet: -0.97 (0.49), residues: 120 loop : -1.70 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 225 HIS 0.004 0.001 HIS C 77 PHE 0.009 0.001 PHE B 217 TYR 0.009 0.001 TYR B 323 ARG 0.003 0.000 ARG D 257 =============================================================================== Job complete usr+sys time: 1728.23 seconds wall clock time: 32 minutes 40.48 seconds (1960.48 seconds total)