Starting phenix.real_space_refine on Tue Nov 14 22:51:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/11_2023/7wut_32841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/11_2023/7wut_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_32841/11_2023/7wut_32841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/11_2023/7wut_32841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/11_2023/7wut_32841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wut_32841/11_2023/7wut_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-1.21rc1-5144/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: 5.45, per 1000 atoms: 0.56 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: 3.73 Conformation dependent library (CDL) restraints added in 1.7 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: 0.99 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: 2.26 Time building geometry restraints manager: 4.02 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 1.480 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.990 Find NCS groups from input model: 0.580 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.156 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.1720 time to fit residues: 20.0385 Evaluate side-chains 74 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1201 time to fit residues: 1.7583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0000 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: 5.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 overall best weight: 3.3390 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9964 Z= 0.277 Angle : 0.802 10.304 13520 Z= 0.415 Chirality : 0.046 0.185 1480 Planarity : 0.004 0.032 1740 Dihedral : 5.208 22.717 1340 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.74 % Favored : 84.94 % Rotamer: Outliers : 3.91 % Allowed : 29.98 % Favored : 66.11 % 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: -1.89 (0.24), residues: 1248 helix: 0.01 (0.44), residues: 144 sheet: -1.10 (0.57), residues: 96 loop : -1.60 (0.21), residues: 1008 *********************** 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 119 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 79 time to evaluate : 1.052 Fit side-chains outliers start: 40 outliers final: 13 residues processed: 108 average time/residue: 0.1679 time to fit residues: 28.1981 Evaluate side-chains 93 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1213 time to fit residues: 4.4795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 111 optimal weight: 0.2980 chunk 38 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.1381 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= 0.312 Angle : 0.834 10.181 13520 Z= 0.428 Chirality : 0.047 0.173 1480 Planarity : 0.004 0.031 1740 Dihedral : 5.465 25.564 1340 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.66 % Favored : 85.02 % Rotamer: Outliers : 3.52 % Allowed : 29.79 % Favored : 66.70 % 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: -1.97 (0.24), residues: 1248 helix: 0.17 (0.46), residues: 144 sheet: -1.22 (0.55), residues: 100 loop : -1.69 (0.20), residues: 1004 *********************** 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 120 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 1.214 Fit side-chains outliers start: 36 outliers final: 14 residues processed: 115 average time/residue: 0.1927 time to fit residues: 33.0667 Evaluate side-chains 93 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1006 time to fit residues: 4.0090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.1490 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= 0.246 Angle : 0.807 10.529 13520 Z= 0.414 Chirality : 0.046 0.191 1480 Planarity : 0.004 0.034 1740 Dihedral : 5.376 25.001 1340 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.42 % Favored : 85.26 % Rotamer: Outliers : 1.46 % Allowed : 32.62 % Favored : 65.92 % 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: -1.87 (0.24), residues: 1248 helix: 0.23 (0.47), residues: 144 sheet: -0.61 (0.57), residues: 92 loop : -1.68 (0.20), residues: 1012 *********************** 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 103 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.087 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 99 average time/residue: 0.1637 time to fit residues: 25.8102 Evaluate side-chains 85 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0880 time to fit residues: 2.2805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 102 optimal weight: 30.0000 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.1786 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= 0.326 Angle : 0.855 10.169 13520 Z= 0.436 Chirality : 0.047 0.187 1480 Planarity : 0.004 0.034 1740 Dihedral : 5.526 24.586 1340 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 15.62 % Favored : 84.05 % Rotamer: Outliers : 2.54 % Allowed : 33.59 % 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: -1.94 (0.24), residues: 1248 helix: 0.26 (0.47), residues: 144 sheet: -1.00 (0.57), residues: 100 loop : -1.70 (0.20), residues: 1004 *********************** 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 108 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 1.208 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 105 average time/residue: 0.1615 time to fit residues: 27.0160 Evaluate side-chains 95 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0913 time to fit residues: 4.0698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1818 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= 0.299 Angle : 0.853 10.259 13520 Z= 0.439 Chirality : 0.047 0.181 1480 Planarity : 0.004 0.034 1740 Dihedral : 5.552 24.389 1340 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.50 % Favored : 85.18 % Rotamer: Outliers : 1.37 % Allowed : 33.69 % Favored : 64.94 % 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 (0.24), residues: 1248 helix: 0.29 (0.46), residues: 144 sheet: -0.81 (0.58), residues: 100 loop : -1.72 (0.20), residues: 1004 *********************** 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 99 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.165 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 96 average time/residue: 0.1769 time to fit residues: 26.8768 Evaluate side-chains 83 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0960 time to fit residues: 2.5602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.7980 chunk 13 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2003 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= 0.331 Angle : 0.876 10.198 13520 Z= 0.450 Chirality : 0.048 0.180 1480 Planarity : 0.004 0.033 1740 Dihedral : 5.676 24.048 1340 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.32 % Allowed : 16.51 % Favored : 83.17 % Rotamer: Outliers : 0.98 % Allowed : 34.77 % Favored : 64.26 % 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 (0.24), residues: 1248 helix: 0.33 (0.47), residues: 144 sheet: -1.03 (0.58), residues: 104 loop : -1.74 (0.20), residues: 1000 *********************** 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 90 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.226 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 85 average time/residue: 0.1861 time to fit residues: 25.0114 Evaluate side-chains 80 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1086 time to fit residues: 1.9174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.1998 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= 0.290 Angle : 0.856 10.284 13520 Z= 0.438 Chirality : 0.047 0.180 1480 Planarity : 0.004 0.033 1740 Dihedral : 5.557 24.073 1340 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.74 % Favored : 84.94 % Rotamer: Outliers : 1.27 % Allowed : 34.08 % Favored : 64.65 % 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 (0.24), residues: 1248 helix: 0.36 (0.47), residues: 144 sheet: -1.15 (0.57), residues: 104 loop : -1.73 (0.20), residues: 1000 *********************** 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 96 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.212 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 91 average time/residue: 0.1755 time to fit residues: 25.1132 Evaluate side-chains 86 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1021 time to fit residues: 2.6238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.2143 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= 0.335 Angle : 0.888 10.266 13520 Z= 0.453 Chirality : 0.048 0.179 1480 Planarity : 0.004 0.033 1740 Dihedral : 5.679 23.858 1340 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 16.03 % Favored : 83.65 % Rotamer: Outliers : 0.29 % Allowed : 34.96 % Favored : 64.75 % 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: -2.02 (0.24), residues: 1248 helix: 0.27 (0.46), residues: 144 sheet: -1.20 (0.57), residues: 104 loop : -1.76 (0.20), residues: 1000 *********************** 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 81 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.222 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 78 average time/residue: 0.1731 time to fit residues: 21.6734 Evaluate side-chains 79 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1276 time to fit residues: 1.8019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.0070 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN B 77 HIS C 76 ASN D 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9964 Z= 0.231 Angle : 0.852 10.302 13520 Z= 0.429 Chirality : 0.047 0.178 1480 Planarity : 0.004 0.033 1740 Dihedral : 5.378 24.132 1340 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.70 % Favored : 85.98 % Rotamer: Outliers : 0.00 % Allowed : 35.25 % Favored : 64.75 % 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 (0.24), residues: 1248 helix: 0.07 (0.46), residues: 148 sheet: -0.66 (0.62), residues: 92 loop : -1.70 (0.20), residues: 1008 ********************** 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 82 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.384 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1715 time to fit residues: 22.3696 Evaluate side-chains 77 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0670 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 0.0870 chunk 98 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.115843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.080244 restraints weight = 33275.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.083258 restraints weight = 17598.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.085302 restraints weight = 12057.896| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.003 0.038 9964 Z= 0.206 Angle : 0.845 10.530 13520 Z= 0.424 Chirality : 0.047 0.176 1480 Planarity : 0.004 0.032 1740 Dihedral : 5.179 28.014 1340 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.70 % Favored : 85.98 % Rotamer: Outliers : 0.49 % Allowed : 34.77 % Favored : 64.75 % 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: -1.85 (0.24), residues: 1248 helix: 0.02 (0.46), residues: 148 sheet: -0.30 (0.62), residues: 84 loop : -1.66 (0.20), residues: 1016 =============================================================================== Job complete usr+sys time: 1657.10 seconds wall clock time: 31 minutes 32.77 seconds (1892.77 seconds total)