Starting phenix.real_space_refine on Fri Dec 8 06:38:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/12_2023/8jv5_36668_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/12_2023/8jv5_36668.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/12_2023/8jv5_36668_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/12_2023/8jv5_36668_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/12_2023/8jv5_36668_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/12_2023/8jv5_36668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/12_2023/8jv5_36668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/12_2023/8jv5_36668_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv5_36668/12_2023/8jv5_36668_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.094 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: 5 Type Number sf(0) Gaussians Br 6 7.06 5 S 51 5.16 5 C 4733 2.51 5 N 1249 2.21 5 O 1441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2428 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 297} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2428 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 297} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2435 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 298} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'P73': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'P73': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'NAG': 3, 'P73': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.42, per 1000 atoms: 0.59 Number of scatterers: 7480 At special positions: 0 Unit cell: (91.3, 85.49, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 6 34.99 S 51 16.00 O 1441 8.00 N 1249 7.00 C 4733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 273 " distance=2.02 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 264 " - pdb=" SG CYS C 273 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 213 " " NAG A 503 " - " ASN A 187 " " NAG A 504 " - " ASN A 78 " " NAG B 502 " - " ASN B 213 " " NAG B 503 " - " ASN B 187 " " NAG B 504 " - " ASN B 78 " " NAG C 502 " - " ASN C 213 " " NAG C 503 " - " ASN C 187 " " NAG C 504 " - " ASN C 78 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 18 sheets defined 17.5% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 235 through 242 removed outlier: 3.760A pdb=" N ALA A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 4.102A pdb=" N ARG A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 235 through 242 removed outlier: 3.763A pdb=" N ALA B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 4.105A pdb=" N ARG B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 336 through 357 Processing helix chain 'C' and resid 43 through 49 removed outlier: 3.803A pdb=" N ILE C 47 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 186 Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 235 through 242 removed outlier: 3.762A pdb=" N ALA C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 4.110A pdb=" N ARG C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 336 through 357 Processing sheet with id= A, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.784A pdb=" N GLY A 254 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASP A 323 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET A 256 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET A 325 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL A 258 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE A 327 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE A 260 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLN A 329 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP A 262 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY A 331 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N CYS A 264 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N PHE A 333 " --> pdb=" O CYS A 264 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 64 through 72 Processing sheet with id= C, first strand: chain 'A' and resid 75 through 77 Processing sheet with id= D, first strand: chain 'A' and resid 115 through 120 Processing sheet with id= E, first strand: chain 'A' and resid 195 through 198 Processing sheet with id= F, first strand: chain 'A' and resid 296 through 304 removed outlier: 6.330A pdb=" N ILE A 320 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 105 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE A 322 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 103 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.784A pdb=" N GLY B 254 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASP B 323 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET B 256 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N MET B 325 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 258 " --> pdb=" O MET B 325 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE B 327 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE B 260 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN B 329 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP B 262 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLY B 331 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N CYS B 264 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N PHE B 333 " --> pdb=" O CYS B 264 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 64 through 72 Processing sheet with id= I, first strand: chain 'B' and resid 75 through 77 Processing sheet with id= J, first strand: chain 'B' and resid 115 through 120 Processing sheet with id= K, first strand: chain 'B' and resid 195 through 198 Processing sheet with id= L, first strand: chain 'B' and resid 296 through 304 removed outlier: 6.334A pdb=" N ILE B 320 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 105 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE B 322 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE B 103 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.769A pdb=" N GLY C 254 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASP C 323 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET C 256 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET C 325 " --> pdb=" O MET C 256 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 258 " --> pdb=" O MET C 325 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE C 327 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE C 260 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLN C 329 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP C 262 " --> pdb=" O GLN C 329 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY C 331 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N CYS C 264 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N PHE C 333 " --> pdb=" O CYS C 264 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 64 through 72 Processing sheet with id= O, first strand: chain 'C' and resid 75 through 77 Processing sheet with id= P, first strand: chain 'C' and resid 115 through 120 Processing sheet with id= Q, first strand: chain 'C' and resid 195 through 198 Processing sheet with id= R, first strand: chain 'C' and resid 296 through 304 removed outlier: 6.333A pdb=" N ILE C 320 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU C 105 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE C 322 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE C 103 " --> pdb=" O PHE C 322 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 621 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2065 1.33 - 1.48: 2359 1.48 - 1.63: 3155 1.63 - 1.79: 7 1.79 - 1.94: 65 Bond restraints: 7651 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" C15 P73 B 501 " pdb=" N14 P73 B 501 " ideal model delta sigma weight residual 1.351 1.317 0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C13 P73 C 501 " pdb=" N14 P73 C 501 " ideal model delta sigma weight residual 1.352 1.319 0.033 2.00e-02 2.50e+03 2.80e+00 bond pdb=" C13 P73 A 501 " pdb=" N14 P73 A 501 " ideal model delta sigma weight residual 1.352 1.319 0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C15 P73 C 501 " pdb=" N14 P73 C 501 " ideal model delta sigma weight residual 1.351 1.318 0.033 2.00e-02 2.50e+03 2.69e+00 ... (remaining 7646 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 249 106.67 - 113.50: 4149 113.50 - 120.32: 2731 120.32 - 127.15: 3237 127.15 - 133.98: 72 Bond angle restraints: 10438 Sorted by residual: angle pdb=" C06 P73 C 501 " pdb=" C08 P73 C 501 " pdb=" N09 P73 C 501 " ideal model delta sigma weight residual 88.20 122.03 -33.83 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C06 P73 B 501 " pdb=" C08 P73 B 501 " pdb=" N09 P73 B 501 " ideal model delta sigma weight residual 88.20 121.96 -33.76 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C06 P73 A 501 " pdb=" C08 P73 A 501 " pdb=" N09 P73 A 501 " ideal model delta sigma weight residual 88.20 121.96 -33.76 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C19 P73 C 501 " pdb=" C08 P73 C 501 " pdb=" N09 P73 C 501 " ideal model delta sigma weight residual 140.96 118.17 22.79 3.00e+00 1.11e-01 5.77e+01 angle pdb=" C19 P73 B 501 " pdb=" C08 P73 B 501 " pdb=" N09 P73 B 501 " ideal model delta sigma weight residual 140.96 118.26 22.70 3.00e+00 1.11e-01 5.72e+01 ... (remaining 10433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 4206 15.23 - 30.47: 341 30.47 - 45.70: 80 45.70 - 60.94: 24 60.94 - 76.17: 12 Dihedral angle restraints: 4663 sinusoidal: 1918 harmonic: 2745 Sorted by residual: dihedral pdb=" CB CYS C 220 " pdb=" SG CYS C 220 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual 93.00 157.49 -64.49 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual 93.00 157.43 -64.43 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual 93.00 157.33 -64.33 1 1.00e+01 1.00e-02 5.44e+01 ... (remaining 4660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 638 0.026 - 0.053: 315 0.053 - 0.079: 106 0.079 - 0.106: 85 0.106 - 0.132: 46 Chirality restraints: 1190 Sorted by residual: chirality pdb=" CA ILE B 94 " pdb=" N ILE B 94 " pdb=" C ILE B 94 " pdb=" CB ILE B 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE C 94 " pdb=" N ILE C 94 " pdb=" C ILE C 94 " pdb=" CB ILE C 94 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1187 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 198 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO C 199 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 199 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 199 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 198 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 199 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 198 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO B 199 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " 0.023 5.00e-02 4.00e+02 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2293 2.83 - 3.35: 6449 3.35 - 3.86: 11723 3.86 - 4.38: 13758 4.38 - 4.90: 24143 Nonbonded interactions: 58366 Sorted by model distance: nonbonded pdb=" NE ARG B 281 " pdb=" OD1 ASP B 283 " model vdw 2.312 2.520 nonbonded pdb=" NE ARG A 281 " pdb=" OD1 ASP A 283 " model vdw 2.318 2.520 nonbonded pdb=" OD2 ASP B 99 " pdb=" OH TYR C 295 " model vdw 2.322 2.440 nonbonded pdb=" NE ARG C 281 " pdb=" OD1 ASP C 283 " model vdw 2.322 2.520 nonbonded pdb=" OD2 ASP A 99 " pdb=" OH TYR B 295 " model vdw 2.326 2.440 ... (remaining 58361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 43 through 358 or resid 501 through 504)) } 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: 0.950 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: 3.860 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.410 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 0.034 7651 Z= 0.270 Angle : 0.910 33.827 10438 Z= 0.388 Chirality : 0.045 0.132 1190 Planarity : 0.005 0.044 1354 Dihedral : 12.595 76.169 2858 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.76 % Allowed : 3.29 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.88 (0.27), residues: 943 helix: 1.17 (0.44), residues: 174 sheet: 1.29 (0.29), residues: 330 loop : -0.16 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 262 HIS 0.000 0.000 HIS B 132 PHE 0.011 0.001 PHE B 327 TYR 0.008 0.001 TYR C 318 ARG 0.003 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 155 average time/residue: 0.2473 time to fit residues: 48.7188 Evaluate side-chains 94 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 247 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 7651 Z= 0.517 Angle : 0.729 7.829 10438 Z= 0.378 Chirality : 0.049 0.137 1190 Planarity : 0.006 0.043 1354 Dihedral : 6.893 46.014 1222 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.90 % Allowed : 12.41 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.38 (0.27), residues: 943 helix: 0.78 (0.42), residues: 177 sheet: 1.08 (0.28), residues: 325 loop : -0.58 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP C 87 HIS 0.001 0.000 HIS A 132 PHE 0.024 0.003 PHE B 103 TYR 0.016 0.002 TYR B 57 ARG 0.005 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.2246 time to fit residues: 31.2576 Evaluate side-chains 102 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0960 time to fit residues: 3.0381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7651 Z= 0.179 Angle : 0.571 7.582 10438 Z= 0.291 Chirality : 0.044 0.133 1190 Planarity : 0.004 0.039 1354 Dihedral : 5.968 39.700 1222 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.38 % Allowed : 14.56 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.58 (0.27), residues: 943 helix: 1.15 (0.43), residues: 175 sheet: 1.22 (0.29), residues: 334 loop : -0.61 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 272 HIS 0.000 0.000 HIS C 132 PHE 0.010 0.001 PHE C 103 TYR 0.012 0.001 TYR C 318 ARG 0.004 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.954 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 95 average time/residue: 0.2495 time to fit residues: 30.7475 Evaluate side-chains 87 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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: 0.8031 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 7651 Z= 0.420 Angle : 0.689 10.395 10438 Z= 0.350 Chirality : 0.046 0.142 1190 Planarity : 0.005 0.044 1354 Dihedral : 5.814 27.622 1222 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.04 % Allowed : 14.94 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.22 (0.27), residues: 943 helix: 0.91 (0.42), residues: 174 sheet: 0.73 (0.28), residues: 342 loop : -0.62 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 272 HIS 0.000 0.000 HIS B 132 PHE 0.020 0.002 PHE B 103 TYR 0.012 0.002 TYR A 57 ARG 0.004 0.001 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 108 average time/residue: 0.2524 time to fit residues: 35.5946 Evaluate side-chains 101 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0808 time to fit residues: 3.3258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7651 Z= 0.203 Angle : 0.591 8.826 10438 Z= 0.299 Chirality : 0.044 0.126 1190 Planarity : 0.004 0.043 1354 Dihedral : 5.310 24.943 1222 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.27 % Allowed : 16.96 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.35 (0.27), residues: 943 helix: 1.03 (0.43), residues: 173 sheet: 1.06 (0.29), residues: 330 loop : -0.74 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 167 HIS 0.000 0.000 HIS A 132 PHE 0.011 0.001 PHE C 103 TYR 0.008 0.001 TYR B 92 ARG 0.002 0.000 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.864 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 0.2413 time to fit residues: 30.8999 Evaluate side-chains 88 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0660 time to fit residues: 1.6074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 7651 Z= 0.581 Angle : 0.757 8.998 10438 Z= 0.389 Chirality : 0.049 0.158 1190 Planarity : 0.005 0.044 1354 Dihedral : 5.796 26.619 1222 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.66 % Allowed : 16.96 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -0.10 (0.27), residues: 943 helix: 0.72 (0.43), residues: 174 sheet: 0.41 (0.28), residues: 342 loop : -0.74 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 87 HIS 0.001 0.000 HIS B 132 PHE 0.024 0.003 PHE B 103 TYR 0.013 0.002 TYR A 57 ARG 0.004 0.001 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.829 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 91 average time/residue: 0.2644 time to fit residues: 30.9075 Evaluate side-chains 88 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0675 time to fit residues: 2.6309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 0.0030 chunk 89 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 54 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7651 Z= 0.153 Angle : 0.586 8.582 10438 Z= 0.297 Chirality : 0.044 0.134 1190 Planarity : 0.004 0.044 1354 Dihedral : 5.124 22.806 1222 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.51 % Allowed : 18.23 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.31 (0.27), residues: 943 helix: 0.95 (0.43), residues: 173 sheet: 1.17 (0.28), residues: 323 loop : -0.82 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 262 HIS 0.001 0.001 HIS A 132 PHE 0.013 0.001 PHE C 103 TYR 0.013 0.001 TYR C 318 ARG 0.006 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.836 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 104 average time/residue: 0.2467 time to fit residues: 33.3392 Evaluate side-chains 93 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0901 time to fit residues: 1.5131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7963 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7651 Z= 0.191 Angle : 0.588 8.218 10438 Z= 0.296 Chirality : 0.044 0.131 1190 Planarity : 0.004 0.039 1354 Dihedral : 5.014 27.874 1222 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.51 % Allowed : 19.49 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.32 (0.27), residues: 943 helix: 0.97 (0.43), residues: 173 sheet: 0.99 (0.28), residues: 332 loop : -0.70 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 167 HIS 0.000 0.000 HIS C 132 PHE 0.011 0.001 PHE C 103 TYR 0.009 0.001 TYR A 318 ARG 0.005 0.000 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.869 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 91 average time/residue: 0.2578 time to fit residues: 30.3346 Evaluate side-chains 89 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0664 time to fit residues: 1.4810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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: 0.8046 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 7651 Z= 0.419 Angle : 0.692 8.400 10438 Z= 0.353 Chirality : 0.047 0.145 1190 Planarity : 0.005 0.041 1354 Dihedral : 5.434 27.077 1222 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.01 % Allowed : 19.11 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.03 (0.27), residues: 943 helix: 0.88 (0.42), residues: 171 sheet: 0.56 (0.28), residues: 334 loop : -0.71 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 272 HIS 0.000 0.000 HIS C 132 PHE 0.020 0.002 PHE B 103 TYR 0.009 0.002 TYR C 216 ARG 0.005 0.001 ARG C 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.829 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.2666 time to fit residues: 29.1732 Evaluate side-chains 86 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0682 time to fit residues: 1.9756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7651 Z= 0.225 Angle : 0.615 8.144 10438 Z= 0.311 Chirality : 0.044 0.135 1190 Planarity : 0.004 0.041 1354 Dihedral : 5.186 27.250 1222 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.13 % Allowed : 19.87 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.19 (0.27), residues: 943 helix: 1.20 (0.43), residues: 165 sheet: 0.88 (0.28), residues: 324 loop : -0.84 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 262 HIS 0.000 0.000 HIS B 132 PHE 0.011 0.001 PHE C 103 TYR 0.013 0.001 TYR C 318 ARG 0.004 0.000 ARG B 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.840 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.2773 time to fit residues: 28.8442 Evaluate side-chains 78 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0706 time to fit residues: 1.2526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.184157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119388 restraints weight = 6860.717| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.84 r_work: 0.3146 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7651 Z= 0.263 Angle : 0.618 8.066 10438 Z= 0.312 Chirality : 0.045 0.132 1190 Planarity : 0.004 0.040 1354 Dihedral : 5.177 26.701 1222 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.13 % Allowed : 20.38 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.16 (0.27), residues: 943 helix: 1.25 (0.44), residues: 165 sheet: 0.78 (0.28), residues: 326 loop : -0.83 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 262 HIS 0.000 0.000 HIS C 132 PHE 0.012 0.002 PHE B 103 TYR 0.007 0.001 TYR C 57 ARG 0.006 0.001 ARG C 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1896.43 seconds wall clock time: 34 minutes 51.41 seconds (2091.41 seconds total)