Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 08:19:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/04_2023/7v21_31633.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/04_2023/7v21_31633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/04_2023/7v21_31633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/04_2023/7v21_31633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/04_2023/7v21_31633.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/04_2023/7v21_31633.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 7646 2.51 5 N 1996 2.21 5 O 2197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B ASP 476": "OD1" <-> "OD2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 245": "OD1" <-> "OD2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 440": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11903 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2986 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 360} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2990 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 360} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2959 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 356} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2968 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 357} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 6.62, per 1000 atoms: 0.56 Number of scatterers: 11903 At special positions: 0 Unit cell: (109.61, 90.21, 145.5, 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 64 16.00 O 2197 8.00 N 1996 7.00 C 7646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.70 Conformation dependent library (CDL) restraints added in 2.1 seconds 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 37.9% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 106 through 123 Processing helix chain 'A' and resid 164 through 180 removed outlier: 3.884A pdb=" N SER A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.697A pdb=" N SER A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 259 through 274 removed outlier: 3.552A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.728A pdb=" N TRP A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 362 removed outlier: 4.973A pdb=" N GLY A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASN A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 164 through 180 removed outlier: 3.846A pdb=" N SER B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.610A pdb=" N SER B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 337 through 354 Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'C' and resid 106 through 123 removed outlier: 3.526A pdb=" N SER C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 180 removed outlier: 3.834A pdb=" N SER C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.632A pdb=" N SER C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 259 through 274 removed outlier: 3.535A pdb=" N THR C 263 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 325 through 329 removed outlier: 3.692A pdb=" N TRP C 329 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 354 Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'D' and resid 106 through 123 removed outlier: 3.534A pdb=" N SER D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 180 removed outlier: 3.894A pdb=" N SER D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 209 through 215 removed outlier: 3.997A pdb=" N SER D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.556A pdb=" N THR D 263 " --> pdb=" O THR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.834A pdb=" N TRP D 329 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 355 removed outlier: 4.572A pdb=" N GLY D 355 " --> pdb=" O GLY D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 464 through 479 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.474A pdb=" N VAL A 152 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 133 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162 removed outlier: 4.499A pdb=" N PHE A 334 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 201 removed outlier: 4.549A pdb=" N LYS A 199 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.564A pdb=" N VAL B 152 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 133 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 162 removed outlier: 4.044A pdb=" N PHE B 334 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 201 removed outlier: 4.538A pdb=" N LYS B 199 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 309 through 311 Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.591A pdb=" N VAL C 152 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL C 133 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.501A pdb=" N MET C 160 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE C 334 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 201 removed outlier: 4.381A pdb=" N LYS C 199 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 309 through 311 Processing sheet with id=AB4, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.571A pdb=" N VAL D 152 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 133 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.944A pdb=" N PHE D 334 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AB7, first strand: chain 'D' and resid 309 through 311 535 hydrogen bonds defined for protein. 1491 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: 3.69 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3336 1.33 - 1.45: 1992 1.45 - 1.57: 6741 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 12177 Sorted by residual: bond pdb=" C LEU B 365 " pdb=" N PRO B 366 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.22e-02 6.72e+03 6.76e+00 bond pdb=" C LEU A 365 " pdb=" N PRO A 366 " ideal model delta sigma weight residual 1.331 1.361 -0.030 1.31e-02 5.83e+03 5.29e+00 bond pdb=" C LYS B 370 " pdb=" N PRO B 371 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.28e-02 6.10e+03 4.96e+00 bond pdb=" CA PRO C 447 " pdb=" C PRO C 447 " ideal model delta sigma weight residual 1.517 1.531 -0.014 6.70e-03 2.23e+04 4.32e+00 bond pdb=" N ASN B 359 " pdb=" CA ASN B 359 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.05e+00 ... (remaining 12172 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.44: 374 106.44 - 113.36: 6516 113.36 - 120.28: 4426 120.28 - 127.20: 5025 127.20 - 134.12: 141 Bond angle restraints: 16482 Sorted by residual: angle pdb=" N ASN B 363 " pdb=" CA ASN B 363 " pdb=" C ASN B 363 " ideal model delta sigma weight residual 113.16 103.23 9.93 1.24e+00 6.50e-01 6.41e+01 angle pdb=" N ALA A 163 " pdb=" CA ALA A 163 " pdb=" C ALA A 163 " ideal model delta sigma weight residual 111.36 119.81 -8.45 1.09e+00 8.42e-01 6.01e+01 angle pdb=" N ASN A 363 " pdb=" CA ASN A 363 " pdb=" C ASN A 363 " ideal model delta sigma weight residual 111.71 103.14 8.57 1.34e+00 5.57e-01 4.09e+01 angle pdb=" N SER A 360 " pdb=" CA SER A 360 " pdb=" C SER A 360 " ideal model delta sigma weight residual 111.14 117.40 -6.26 1.08e+00 8.57e-01 3.36e+01 angle pdb=" N ALA B 105 " pdb=" CA ALA B 105 " pdb=" C ALA B 105 " ideal model delta sigma weight residual 111.07 117.09 -6.02 1.07e+00 8.73e-01 3.16e+01 ... (remaining 16477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 6588 18.00 - 36.00: 582 36.00 - 53.99: 89 53.99 - 71.99: 21 71.99 - 89.99: 4 Dihedral angle restraints: 7284 sinusoidal: 2927 harmonic: 4357 Sorted by residual: dihedral pdb=" C ASN B 359 " pdb=" N ASN B 359 " pdb=" CA ASN B 359 " pdb=" CB ASN B 359 " ideal model delta harmonic sigma weight residual -122.60 -131.42 8.82 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" CA ASP C 476 " pdb=" CB ASP C 476 " pdb=" CG ASP C 476 " pdb=" OD1 ASP C 476 " ideal model delta sinusoidal sigma weight residual -30.00 -89.32 59.32 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP B 324 " pdb=" CB ASP B 324 " pdb=" CG ASP B 324 " pdb=" OD1 ASP B 324 " ideal model delta sinusoidal sigma weight residual -30.00 -88.42 58.42 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 7281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1447 0.060 - 0.120: 296 0.120 - 0.180: 57 0.180 - 0.240: 11 0.240 - 0.300: 2 Chirality restraints: 1813 Sorted by residual: chirality pdb=" CA ALA A 163 " pdb=" N ALA A 163 " pdb=" C ALA A 163 " pdb=" CB ALA A 163 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ASN B 359 " pdb=" N ASN B 359 " pdb=" C ASN B 359 " pdb=" CB ASN B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA MET D 396 " pdb=" N MET D 396 " pdb=" C MET D 396 " pdb=" CB MET D 396 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1810 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 155 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO D 156 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 155 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 156 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 155 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO B 156 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.021 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2838 2.79 - 3.32: 10843 3.32 - 3.85: 19360 3.85 - 4.37: 24340 4.37 - 4.90: 41144 Nonbonded interactions: 98525 Sorted by model distance: nonbonded pdb=" NH2 ARG D 106 " pdb=" OE1 GLU D 474 " model vdw 2.266 2.520 nonbonded pdb=" O PHE A 260 " pdb=" OG1 THR A 263 " model vdw 2.283 2.440 nonbonded pdb=" O PHE C 260 " pdb=" OG1 THR C 263 " model vdw 2.301 2.440 nonbonded pdb=" OH TYR A 223 " pdb=" OD2 ASP A 245 " model vdw 2.308 2.440 nonbonded pdb=" O PHE D 260 " pdb=" OG1 THR D 263 " model vdw 2.313 2.440 ... (remaining 98520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 103 through 357 or resid 362 through 480)) selection = (chain 'B' and (resid 103 through 357 or (resid 362 and (name N or name CA or na \ me C or name O or name CB )) or resid 363 through 480)) selection = (chain 'C' and (resid 103 through 357 or (resid 362 and (name N or name CA or na \ me C or name O or name CB )) or resid 363 through 480)) selection = (chain 'D' and (resid 103 through 357 or (resid 362 and (name N or name CA or na \ me C or name O or name CB )) or resid 363 through 480)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.620 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.830 Find NCS groups from input model: 0.840 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.004 0.042 12177 Z= 0.247 Angle : 0.732 9.930 16482 Z= 0.451 Chirality : 0.054 0.300 1813 Planarity : 0.004 0.039 2090 Dihedral : 13.476 89.992 4506 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1493 helix: 1.73 (0.24), residues: 499 sheet: 0.66 (0.39), residues: 187 loop : -0.01 (0.22), residues: 807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.550 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 141 average time/residue: 0.3066 time to fit residues: 59.1587 Evaluate side-chains 104 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 HIS C 413 GLN C 419 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 12177 Z= 0.273 Angle : 0.554 6.557 16482 Z= 0.293 Chirality : 0.045 0.135 1813 Planarity : 0.004 0.042 2090 Dihedral : 4.433 19.818 1651 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1493 helix: 1.67 (0.23), residues: 516 sheet: 0.75 (0.39), residues: 187 loop : 0.00 (0.22), residues: 790 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.484 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 121 average time/residue: 0.2534 time to fit residues: 44.3934 Evaluate side-chains 105 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1072 time to fit residues: 2.8390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 325 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 12177 Z= 0.385 Angle : 0.613 7.516 16482 Z= 0.321 Chirality : 0.048 0.177 1813 Planarity : 0.004 0.045 2090 Dihedral : 4.685 20.649 1651 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1493 helix: 1.46 (0.23), residues: 520 sheet: 0.72 (0.38), residues: 190 loop : -0.15 (0.21), residues: 783 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.348 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 120 average time/residue: 0.2670 time to fit residues: 46.2482 Evaluate side-chains 108 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1153 time to fit residues: 3.2427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 0.0040 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS B 419 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12177 Z= 0.181 Angle : 0.493 6.221 16482 Z= 0.262 Chirality : 0.042 0.126 1813 Planarity : 0.003 0.044 2090 Dihedral : 4.347 19.994 1651 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.22), residues: 1493 helix: 1.80 (0.24), residues: 520 sheet: 0.88 (0.39), residues: 193 loop : -0.03 (0.22), residues: 780 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 1.484 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 119 average time/residue: 0.2543 time to fit residues: 44.0236 Evaluate side-chains 105 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2065 time to fit residues: 3.5272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12177 Z= 0.161 Angle : 0.469 5.684 16482 Z= 0.249 Chirality : 0.042 0.126 1813 Planarity : 0.003 0.042 2090 Dihedral : 4.154 18.194 1651 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1493 helix: 1.94 (0.24), residues: 520 sheet: 1.01 (0.40), residues: 189 loop : 0.02 (0.22), residues: 784 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.472 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 108 average time/residue: 0.2508 time to fit residues: 40.2534 Evaluate side-chains 98 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.0770 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 12177 Z= 0.255 Angle : 0.514 6.076 16482 Z= 0.272 Chirality : 0.044 0.129 1813 Planarity : 0.003 0.041 2090 Dihedral : 4.319 18.696 1651 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1493 helix: 1.80 (0.24), residues: 520 sheet: 1.03 (0.40), residues: 187 loop : -0.04 (0.21), residues: 786 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.464 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 110 average time/residue: 0.2565 time to fit residues: 41.0845 Evaluate side-chains 106 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1143 time to fit residues: 2.8377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.1980 chunk 79 optimal weight: 0.0270 chunk 142 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 0.0170 chunk 65 optimal weight: 0.0270 chunk 88 optimal weight: 0.0010 overall best weight: 0.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 12177 Z= 0.109 Angle : 0.429 8.132 16482 Z= 0.229 Chirality : 0.040 0.129 1813 Planarity : 0.003 0.042 2090 Dihedral : 3.872 16.811 1651 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1493 helix: 2.23 (0.24), residues: 504 sheet: 1.14 (0.40), residues: 195 loop : 0.14 (0.22), residues: 794 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.508 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 125 average time/residue: 0.2312 time to fit residues: 43.2909 Evaluate side-chains 112 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1338 time to fit residues: 2.7642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.0770 chunk 85 optimal weight: 7.9990 chunk 42 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 0.0770 overall best weight: 0.6256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 12177 Z= 0.148 Angle : 0.465 10.468 16482 Z= 0.243 Chirality : 0.042 0.167 1813 Planarity : 0.003 0.038 2090 Dihedral : 3.876 16.767 1651 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1493 helix: 2.18 (0.24), residues: 509 sheet: 1.18 (0.41), residues: 187 loop : 0.19 (0.22), residues: 797 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.388 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 112 average time/residue: 0.2387 time to fit residues: 39.7946 Evaluate side-chains 104 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 0.0170 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 125 optimal weight: 0.2980 chunk 87 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN B 191 HIS ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 12177 Z= 0.127 Angle : 0.441 8.842 16482 Z= 0.233 Chirality : 0.041 0.138 1813 Planarity : 0.003 0.037 2090 Dihedral : 3.832 17.084 1651 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1493 helix: 2.22 (0.24), residues: 509 sheet: 1.14 (0.42), residues: 185 loop : 0.18 (0.22), residues: 799 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.458 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 110 average time/residue: 0.2520 time to fit residues: 40.7651 Evaluate side-chains 108 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1177 time to fit residues: 2.2452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12177 Z= 0.162 Angle : 0.464 9.737 16482 Z= 0.244 Chirality : 0.042 0.137 1813 Planarity : 0.003 0.036 2090 Dihedral : 3.890 17.344 1651 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1493 helix: 2.20 (0.24), residues: 509 sheet: 1.16 (0.41), residues: 187 loop : 0.20 (0.22), residues: 797 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.585 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.2399 time to fit residues: 37.8077 Evaluate side-chains 104 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 0.0370 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 HIS ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.089564 restraints weight = 17550.357| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.62 r_work: 0.2870 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 12177 Z= 0.158 Angle : 0.462 9.508 16482 Z= 0.243 Chirality : 0.042 0.136 1813 Planarity : 0.003 0.037 2090 Dihedral : 3.909 17.713 1651 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1493 helix: 2.20 (0.24), residues: 509 sheet: 1.16 (0.41), residues: 187 loop : 0.21 (0.22), residues: 797 =============================================================================== Job complete usr+sys time: 2384.48 seconds wall clock time: 44 minutes 24.42 seconds (2664.42 seconds total)