Starting phenix.real_space_refine on Thu Feb 15 10:11:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/02_2024/7v21_31633.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/02_2024/7v21_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_31633/02_2024/7v21_31633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/02_2024/7v21_31633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/02_2024/7v21_31633.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v21_31633/02_2024/7v21_31633.pdb" } resolution = 3.08 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= 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-dev-5238/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: 6.92, per 1000 atoms: 0.58 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: 4.67 Conformation dependent library (CDL) restraints added in 2.3 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: 1.25 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: 3.55 Time building geometry restraints manager: 5.06 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.030 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 34.000 Find NCS groups from input model: 0.830 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.270 ------------------------------------------------------------------------------- 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 % Allowed : 1.48 % Favored : 98.21 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 178 HIS 0.003 0.001 HIS D 419 PHE 0.014 0.002 PHE A 357 TYR 0.015 0.002 TYR B 262 ARG 0.003 0.000 ARG C 106 *********************** 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 : 1.472 Fit side-chains REVERT: C 396 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7588 (mtp) REVERT: C 411 ARG cc_start: 0.7367 (ttt90) cc_final: 0.7026 (ptp-170) outliers start: 4 outliers final: 0 residues processed: 141 average time/residue: 0.2870 time to fit residues: 55.5227 Evaluate side-chains 105 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 396 MET 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 D 325 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0992 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= 0.272 Angle : 0.556 6.706 16482 Z= 0.294 Chirality : 0.045 0.140 1813 Planarity : 0.004 0.042 2090 Dihedral : 4.575 35.116 1654 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.70 % Allowed : 5.43 % Favored : 93.87 % 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: 0.96 (0.22), residues: 1493 helix: 1.66 (0.23), residues: 516 sheet: 0.75 (0.39), residues: 187 loop : -0.01 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 178 HIS 0.011 0.001 HIS B 191 PHE 0.013 0.001 PHE B 308 TYR 0.023 0.002 TYR A 201 ARG 0.004 0.001 ARG C 411 *********************** 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 126 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.366 Fit side-chains REVERT: A 211 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8155 (ptp-110) REVERT: C 160 MET cc_start: 0.9077 (mtt) cc_final: 0.8874 (mtt) REVERT: C 411 ARG cc_start: 0.7737 (ttt90) cc_final: 0.7041 (ptp-170) outliers start: 9 outliers final: 4 residues processed: 123 average time/residue: 0.2577 time to fit residues: 45.7190 Evaluate side-chains 110 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL 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: 5.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.8495 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12177 Z= 0.255 Angle : 0.530 6.306 16482 Z= 0.280 Chirality : 0.044 0.131 1813 Planarity : 0.004 0.042 2090 Dihedral : 4.401 19.308 1651 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.09 % Allowed : 7.14 % Favored : 91.77 % 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: 1.02 (0.22), residues: 1493 helix: 1.72 (0.23), residues: 520 sheet: 0.74 (0.38), residues: 192 loop : 0.01 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 178 HIS 0.013 0.001 HIS B 191 PHE 0.012 0.001 PHE B 308 TYR 0.018 0.001 TYR A 201 ARG 0.004 0.000 ARG B 316 *********************** 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 123 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.358 Fit side-chains REVERT: A 211 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8147 (ptp-110) REVERT: C 444 ASN cc_start: 0.7355 (t0) cc_final: 0.7092 (t0) REVERT: D 419 HIS cc_start: 0.9071 (OUTLIER) cc_final: 0.8530 (t70) outliers start: 14 outliers final: 10 residues processed: 121 average time/residue: 0.2488 time to fit residues: 43.4307 Evaluate side-chains 115 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 0.0970 chunk 69 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ** 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: 0.8456 moved from start: 0.1362 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= 0.149 Angle : 0.466 5.400 16482 Z= 0.248 Chirality : 0.042 0.127 1813 Planarity : 0.003 0.041 2090 Dihedral : 4.167 18.813 1651 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.01 % Allowed : 8.39 % Favored : 90.61 % 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: 1.32 (0.22), residues: 1493 helix: 2.13 (0.24), residues: 504 sheet: 0.87 (0.39), residues: 193 loop : 0.12 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.011 0.001 HIS B 191 PHE 0.009 0.001 PHE B 308 TYR 0.020 0.001 TYR A 201 ARG 0.005 0.000 ARG C 411 *********************** 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 127 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.498 Fit side-chains REVERT: D 419 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8370 (t70) outliers start: 13 outliers final: 5 residues processed: 123 average time/residue: 0.2622 time to fit residues: 46.3548 Evaluate side-chains 110 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain D residue 419 HIS 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: 0.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12177 Z= 0.159 Angle : 0.462 5.161 16482 Z= 0.245 Chirality : 0.042 0.127 1813 Planarity : 0.003 0.039 2090 Dihedral : 4.085 18.037 1651 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.01 % Allowed : 9.24 % Favored : 89.75 % 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: 1.38 (0.22), residues: 1493 helix: 2.18 (0.24), residues: 504 sheet: 1.04 (0.40), residues: 189 loop : 0.12 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 178 HIS 0.009 0.001 HIS B 191 PHE 0.010 0.001 PHE B 308 TYR 0.017 0.001 TYR A 201 ARG 0.005 0.000 ARG C 411 *********************** 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 119 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.402 Fit side-chains REVERT: A 270 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: D 419 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8518 (t70) outliers start: 13 outliers final: 9 residues processed: 117 average time/residue: 0.2439 time to fit residues: 41.8388 Evaluate side-chains 113 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8518 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12177 Z= 0.306 Angle : 0.549 6.374 16482 Z= 0.289 Chirality : 0.045 0.142 1813 Planarity : 0.004 0.040 2090 Dihedral : 4.425 22.433 1651 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.32 % Allowed : 9.63 % Favored : 89.05 % 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: 1.07 (0.22), residues: 1493 helix: 1.78 (0.23), residues: 520 sheet: 1.04 (0.39), residues: 188 loop : -0.05 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 398 HIS 0.007 0.001 HIS B 191 PHE 0.014 0.001 PHE B 308 TYR 0.016 0.002 TYR C 262 ARG 0.005 0.000 ARG B 316 *********************** 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 122 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.365 Fit side-chains REVERT: C 396 MET cc_start: 0.8410 (mtp) cc_final: 0.8119 (mtp) REVERT: D 419 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8770 (t70) outliers start: 17 outliers final: 10 residues processed: 118 average time/residue: 0.2504 time to fit residues: 42.8896 Evaluate side-chains 115 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS 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: 0.8980 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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: 0.8462 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12177 Z= 0.138 Angle : 0.460 8.785 16482 Z= 0.244 Chirality : 0.041 0.157 1813 Planarity : 0.003 0.041 2090 Dihedral : 4.129 19.521 1651 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.24 % Allowed : 9.94 % Favored : 88.82 % 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: 1.28 (0.22), residues: 1493 helix: 2.02 (0.24), residues: 520 sheet: 1.02 (0.40), residues: 193 loop : 0.06 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.007 0.001 HIS B 191 PHE 0.009 0.001 PHE B 249 TYR 0.012 0.001 TYR B 262 ARG 0.006 0.000 ARG C 411 *********************** 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 128 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.255 Fit side-chains REVERT: A 270 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: C 396 MET cc_start: 0.8376 (mtp) cc_final: 0.8072 (mtp) REVERT: D 419 HIS cc_start: 0.8984 (OUTLIER) cc_final: 0.8438 (t70) outliers start: 16 outliers final: 8 residues processed: 123 average time/residue: 0.2483 time to fit residues: 44.2869 Evaluate side-chains 117 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12177 Z= 0.168 Angle : 0.464 5.234 16482 Z= 0.247 Chirality : 0.042 0.129 1813 Planarity : 0.003 0.039 2090 Dihedral : 4.077 18.871 1651 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.93 % Allowed : 10.56 % Favored : 88.51 % 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: 1.31 (0.22), residues: 1493 helix: 2.02 (0.24), residues: 520 sheet: 1.07 (0.40), residues: 193 loop : 0.07 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.007 0.001 HIS B 191 PHE 0.010 0.001 PHE B 308 TYR 0.013 0.001 TYR C 262 ARG 0.006 0.000 ARG C 411 *********************** 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 117 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.383 Fit side-chains REVERT: A 270 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: C 396 MET cc_start: 0.8387 (mtp) cc_final: 0.8071 (mtp) REVERT: D 282 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7507 (mm-40) REVERT: D 419 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8622 (t70) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 0.2491 time to fit residues: 41.8633 Evaluate side-chains 111 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 0.0470 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 0.2980 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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: 0.8459 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12177 Z= 0.150 Angle : 0.453 5.153 16482 Z= 0.241 Chirality : 0.042 0.162 1813 Planarity : 0.003 0.039 2090 Dihedral : 4.010 17.739 1651 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.01 % Allowed : 11.02 % Favored : 87.97 % 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: 1.36 (0.22), residues: 1493 helix: 2.07 (0.24), residues: 520 sheet: 1.21 (0.40), residues: 189 loop : 0.07 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.007 0.001 HIS B 191 PHE 0.012 0.001 PHE B 249 TYR 0.013 0.001 TYR C 277 ARG 0.006 0.000 ARG C 411 *********************** 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 120 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.490 Fit side-chains REVERT: A 270 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: A 474 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7054 (mm-30) REVERT: C 396 MET cc_start: 0.8381 (mtp) cc_final: 0.8072 (mtp) REVERT: D 282 GLN cc_start: 0.7745 (tp-100) cc_final: 0.7500 (mm-40) REVERT: D 419 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8540 (t70) outliers start: 13 outliers final: 8 residues processed: 118 average time/residue: 0.2489 time to fit residues: 43.0832 Evaluate side-chains 113 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 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: 0.8462 moved from start: 0.1700 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= 0.158 Angle : 0.457 5.187 16482 Z= 0.243 Chirality : 0.042 0.141 1813 Planarity : 0.003 0.039 2090 Dihedral : 3.994 17.504 1651 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.85 % Allowed : 11.41 % Favored : 87.73 % 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: 1.35 (0.22), residues: 1493 helix: 2.08 (0.24), residues: 520 sheet: 1.22 (0.40), residues: 189 loop : 0.05 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 178 HIS 0.007 0.001 HIS B 191 PHE 0.023 0.001 PHE B 248 TYR 0.013 0.001 TYR C 262 ARG 0.007 0.000 ARG C 411 ********************** 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 113 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.463 Fit side-chains REVERT: A 178 TRP cc_start: 0.8449 (t60) cc_final: 0.8168 (t60) REVERT: A 270 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: A 474 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7059 (mm-30) REVERT: C 396 MET cc_start: 0.8397 (mtp) cc_final: 0.8081 (mtp) REVERT: D 282 GLN cc_start: 0.7743 (tp-100) cc_final: 0.7484 (mm-40) REVERT: D 419 HIS cc_start: 0.8977 (OUTLIER) cc_final: 0.8520 (t70) outliers start: 11 outliers final: 8 residues processed: 111 average time/residue: 0.2409 time to fit residues: 39.2916 Evaluate side-chains 112 residues out of total 1305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 419 HIS 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: 1.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.085874 restraints weight = 17616.296| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.61 r_work: 0.2821 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12177 Z= 0.245 Angle : 0.508 5.749 16482 Z= 0.269 Chirality : 0.044 0.153 1813 Planarity : 0.003 0.039 2090 Dihedral : 4.198 18.088 1651 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.93 % Allowed : 11.72 % Favored : 87.34 % 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: 1.22 (0.22), residues: 1493 helix: 1.94 (0.24), residues: 520 sheet: 1.19 (0.40), residues: 189 loop : -0.02 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 178 HIS 0.009 0.001 HIS B 191 PHE 0.023 0.001 PHE B 248 TYR 0.015 0.001 TYR C 262 ARG 0.007 0.000 ARG C 411 =============================================================================== Job complete usr+sys time: 2427.75 seconds wall clock time: 45 minutes 25.61 seconds (2725.61 seconds total)