Starting phenix.real_space_refine (version: dev) on Tue Apr 5 04:10:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/04_2022/5v4s_8633.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/04_2022/5v4s_8633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/04_2022/5v4s_8633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/04_2022/5v4s_8633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/04_2022/5v4s_8633.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/04_2022/5v4s_8633.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 10756 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2689 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 239 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2689 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 239 Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2689 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 239 Chain: "D" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2689 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 239 Time building chain proxies: 6.67, per 1000 atoms: 0.62 Number of scatterers: 10756 At special positions: 0 Unit cell: (116.067, 116.067, 109.24, 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 24 16.00 O 1896 8.00 N 1844 7.00 C 6992 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: 5.10 Conformation dependent library (CDL) restraints added in 1.8 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2936 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 74.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.040A pdb=" N ILE A 31 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 59 Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.972A pdb=" N VAL A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 removed outlier: 4.416A pdb=" N LEU A 124 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 removed outlier: 4.024A pdb=" N GLN A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 173 Processing helix chain 'A' and resid 179 through 195 Processing helix chain 'A' and resid 206 through 260 removed outlier: 4.881A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 280 removed outlier: 4.172A pdb=" N ARG A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 293 through 310 removed outlier: 3.699A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 319 through 330 Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.884A pdb=" N ILE A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.040A pdb=" N ILE B 31 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 59 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 95 through 104 Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.972A pdb=" N VAL B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 removed outlier: 4.416A pdb=" N LEU B 124 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 125 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 141 removed outlier: 4.025A pdb=" N GLN B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 173 Processing helix chain 'B' and resid 179 through 195 Processing helix chain 'B' and resid 206 through 260 removed outlier: 4.881A pdb=" N LYS B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 280 removed outlier: 4.172A pdb=" N ARG B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 293 through 310 removed outlier: 3.699A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 407 through 417 Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.883A pdb=" N ILE B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 27 Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.040A pdb=" N ILE C 31 " --> pdb=" O PRO C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 59 Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 114 through 120 removed outlier: 3.972A pdb=" N VAL C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 4.416A pdb=" N LEU C 124 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS C 125 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 removed outlier: 4.025A pdb=" N GLN C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 173 Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 206 through 260 removed outlier: 4.881A pdb=" N LYS C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 280 removed outlier: 4.172A pdb=" N ARG C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 293 through 310 removed outlier: 3.699A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 319 through 330 Processing helix chain 'C' and resid 380 through 386 Processing helix chain 'C' and resid 407 through 417 Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.883A pdb=" N ILE C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 429 " --> pdb=" O GLU C 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 27 Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.040A pdb=" N ILE D 31 " --> pdb=" O PRO D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 59 Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 95 through 104 Processing helix chain 'D' and resid 114 through 120 removed outlier: 3.972A pdb=" N VAL D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 removed outlier: 4.416A pdb=" N LEU D 124 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS D 125 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 removed outlier: 4.025A pdb=" N GLN D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 173 Processing helix chain 'D' and resid 179 through 195 Processing helix chain 'D' and resid 206 through 260 removed outlier: 4.881A pdb=" N LYS D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 280 removed outlier: 4.172A pdb=" N ARG D 268 " --> pdb=" O ASN D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 293 through 310 removed outlier: 3.699A pdb=" N LEU D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 380 through 386 Processing helix chain 'D' and resid 407 through 417 Processing helix chain 'D' and resid 417 through 429 removed outlier: 3.883A pdb=" N ILE D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 335 removed outlier: 6.544A pdb=" N GLU A 401 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 340 through 342 removed outlier: 6.530A pdb=" N THR A 340 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA A 396 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 331 through 335 removed outlier: 6.544A pdb=" N GLU B 401 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 340 through 342 removed outlier: 6.531A pdb=" N THR B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA B 396 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 331 through 335 removed outlier: 6.544A pdb=" N GLU C 401 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 340 through 342 removed outlier: 6.531A pdb=" N THR C 340 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA C 396 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 331 through 335 removed outlier: 6.544A pdb=" N GLU D 401 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 340 through 342 removed outlier: 6.531A pdb=" N THR D 340 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA D 396 " --> pdb=" O THR D 340 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2595 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: 3.51 Time building geometry restraints manager: 5.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2224 1.32 - 1.44: 2731 1.44 - 1.56: 5969 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 10960 Sorted by residual: bond pdb=" CA LEU A 322 " pdb=" C LEU A 322 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.27e-02 6.20e+03 1.46e+01 bond pdb=" CA LEU B 322 " pdb=" C LEU B 322 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 bond pdb=" CA LEU C 322 " pdb=" C LEU C 322 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 bond pdb=" CA LEU D 322 " pdb=" C LEU D 322 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 bond pdb=" N PRO C 144 " pdb=" CD PRO C 144 " ideal model delta sigma weight residual 1.473 1.431 0.042 1.40e-02 5.10e+03 8.93e+00 ... (remaining 10955 not shown) Histogram of bond angle deviations from ideal: 89.00 - 99.95: 12 99.95 - 110.91: 4371 110.91 - 121.86: 8190 121.86 - 132.81: 2415 132.81 - 143.76: 48 Bond angle restraints: 15036 Sorted by residual: angle pdb=" N LEU B 96 " pdb=" CA LEU B 96 " pdb=" C LEU B 96 " ideal model delta sigma weight residual 110.80 143.76 -32.96 2.13e+00 2.20e-01 2.39e+02 angle pdb=" N LEU C 96 " pdb=" CA LEU C 96 " pdb=" C LEU C 96 " ideal model delta sigma weight residual 110.80 143.76 -32.96 2.13e+00 2.20e-01 2.39e+02 angle pdb=" N LEU D 96 " pdb=" CA LEU D 96 " pdb=" C LEU D 96 " ideal model delta sigma weight residual 110.80 143.76 -32.96 2.13e+00 2.20e-01 2.39e+02 angle pdb=" N LEU A 96 " pdb=" CA LEU A 96 " pdb=" C LEU A 96 " ideal model delta sigma weight residual 110.80 143.75 -32.95 2.13e+00 2.20e-01 2.39e+02 angle pdb=" N GLU C 97 " pdb=" CA GLU C 97 " pdb=" CB GLU C 97 " ideal model delta sigma weight residual 110.07 89.00 21.07 1.45e+00 4.76e-01 2.11e+02 ... (remaining 15031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.27: 6012 13.27 - 26.54: 180 26.54 - 39.81: 60 39.81 - 53.07: 12 53.07 - 66.34: 12 Dihedral angle restraints: 6276 sinusoidal: 1748 harmonic: 4528 Sorted by residual: dihedral pdb=" C ARG C 30 " pdb=" N ARG C 30 " pdb=" CA ARG C 30 " pdb=" CB ARG C 30 " ideal model delta harmonic sigma weight residual -122.60 -153.91 31.31 0 2.50e+00 1.60e-01 1.57e+02 dihedral pdb=" C ARG D 30 " pdb=" N ARG D 30 " pdb=" CA ARG D 30 " pdb=" CB ARG D 30 " ideal model delta harmonic sigma weight residual -122.60 -153.91 31.31 0 2.50e+00 1.60e-01 1.57e+02 dihedral pdb=" C ARG B 30 " pdb=" N ARG B 30 " pdb=" CA ARG B 30 " pdb=" CB ARG B 30 " ideal model delta harmonic sigma weight residual -122.60 -153.91 31.31 0 2.50e+00 1.60e-01 1.57e+02 ... (remaining 6273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.300: 1816 0.300 - 0.599: 12 0.599 - 0.899: 4 0.899 - 1.199: 0 1.199 - 1.499: 12 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CA LEU A 96 " pdb=" N LEU A 96 " pdb=" C LEU A 96 " pdb=" CB LEU A 96 " both_signs ideal model delta sigma weight residual False 2.51 1.01 1.50 2.00e-01 2.50e+01 5.62e+01 chirality pdb=" CA LEU D 96 " pdb=" N LEU D 96 " pdb=" C LEU D 96 " pdb=" CB LEU D 96 " both_signs ideal model delta sigma weight residual False 2.51 1.01 1.50 2.00e-01 2.50e+01 5.60e+01 chirality pdb=" CA LEU B 96 " pdb=" N LEU B 96 " pdb=" C LEU B 96 " pdb=" CB LEU B 96 " both_signs ideal model delta sigma weight residual False 2.51 1.01 1.50 2.00e-01 2.50e+01 5.60e+01 ... (remaining 1841 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 141 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO D 142 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 141 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO C 142 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 141 " -0.085 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO B 142 " 0.223 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " -0.066 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4445 2.86 - 3.37: 12000 3.37 - 3.88: 17535 3.88 - 4.39: 20739 4.39 - 4.90: 30705 Nonbonded interactions: 85424 Sorted by model distance: nonbonded pdb=" OG1 THR A 101 " pdb=" OH TYR A 115 " model vdw 2.352 2.440 nonbonded pdb=" OG1 THR D 101 " pdb=" OH TYR D 115 " model vdw 2.352 2.440 nonbonded pdb=" OG1 THR C 101 " pdb=" OH TYR C 115 " model vdw 2.352 2.440 nonbonded pdb=" OG1 THR B 101 " pdb=" OH TYR B 115 " model vdw 2.352 2.440 nonbonded pdb=" O ALA A 195 " pdb=" OG1 THR A 196 " model vdw 2.436 2.440 ... (remaining 85419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 6992 2.51 5 N 1844 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.460 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 33.030 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 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 : 0.012 0.062 10960 Z= 0.792 Angle : 1.557 32.963 15036 Z= 1.038 Chirality : 0.138 1.499 1844 Planarity : 0.011 0.129 1888 Dihedral : 8.803 66.342 3340 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.60 % Favored : 93.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 1.36 % Peptide Plane: Cis-proline : 0.00 % 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: -1.95 (0.19), residues: 1516 helix: -0.89 (0.13), residues: 1068 sheet: -1.20 (0.47), residues: 68 loop : -2.00 (0.31), residues: 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2925 time to fit residues: 60.3152 Evaluate side-chains 80 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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: 0.6035 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10960 Z= 0.182 Angle : 0.530 7.165 15036 Z= 0.306 Chirality : 0.038 0.148 1844 Planarity : 0.005 0.062 1888 Dihedral : 4.088 15.699 1652 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.21), residues: 1516 helix: 1.20 (0.15), residues: 1100 sheet: 0.35 (0.66), residues: 52 loop : -0.78 (0.32), residues: 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 121 average time/residue: 0.2596 time to fit residues: 43.3522 Evaluate side-chains 73 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 149 optimal weight: 50.0000 chunk 123 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 230 ASN B 134 GLN B 230 ASN C 134 GLN D 134 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10960 Z= 0.213 Angle : 0.516 5.568 15036 Z= 0.300 Chirality : 0.038 0.130 1844 Planarity : 0.004 0.045 1888 Dihedral : 3.826 14.574 1652 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.21), residues: 1516 helix: 1.64 (0.15), residues: 1096 sheet: 1.02 (0.78), residues: 48 loop : -0.24 (0.35), residues: 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3129 time to fit residues: 43.1924 Evaluate side-chains 63 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.311 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 71 optimal weight: 50.0000 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 chunk 131 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 10960 Z= 0.377 Angle : 0.730 8.447 15036 Z= 0.415 Chirality : 0.043 0.127 1844 Planarity : 0.006 0.060 1888 Dihedral : 4.588 18.064 1652 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.21), residues: 1516 helix: 0.87 (0.14), residues: 1096 sheet: 1.82 (0.73), residues: 56 loop : 0.00 (0.37), residues: 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3308 time to fit residues: 37.4632 Evaluate side-chains 59 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 109 optimal weight: 0.0060 chunk 60 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 245 GLN B 59 ASN B 245 GLN C 59 ASN C 245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 10960 Z= 0.150 Angle : 0.464 4.426 15036 Z= 0.263 Chirality : 0.037 0.129 1844 Planarity : 0.003 0.029 1888 Dihedral : 3.893 17.091 1652 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.19 (0.22), residues: 1516 helix: 1.83 (0.15), residues: 1104 sheet: 0.31 (0.61), residues: 96 loop : 0.69 (0.42), residues: 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2910 time to fit residues: 36.4574 Evaluate side-chains 54 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 50.0000 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 50.0000 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10960 Z= 0.182 Angle : 0.471 4.403 15036 Z= 0.274 Chirality : 0.038 0.137 1844 Planarity : 0.003 0.027 1888 Dihedral : 3.786 16.590 1652 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.48 (0.22), residues: 1516 helix: 2.07 (0.15), residues: 1104 sheet: 0.22 (0.63), residues: 96 loop : 0.78 (0.43), residues: 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2392 time to fit residues: 29.0185 Evaluate side-chains 53 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 107 optimal weight: 50.0000 chunk 123 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS B 161 HIS C 161 HIS ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 10960 Z= 0.161 Angle : 0.466 7.811 15036 Z= 0.263 Chirality : 0.037 0.153 1844 Planarity : 0.003 0.026 1888 Dihedral : 3.577 16.872 1652 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.82 (0.22), residues: 1516 helix: 2.36 (0.15), residues: 1104 sheet: 0.21 (0.64), residues: 96 loop : 0.76 (0.43), residues: 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2176 time to fit residues: 27.8953 Evaluate side-chains 52 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 10960 Z= 0.203 Angle : 0.494 5.045 15036 Z= 0.288 Chirality : 0.038 0.137 1844 Planarity : 0.004 0.028 1888 Dihedral : 3.733 17.319 1652 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.87 (0.23), residues: 1516 helix: 2.36 (0.15), residues: 1108 sheet: 0.18 (0.64), residues: 96 loop : 0.92 (0.44), residues: 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2155 time to fit residues: 26.6342 Evaluate side-chains 54 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 144 optimal weight: 40.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10960 Z= 0.165 Angle : 0.473 6.836 15036 Z= 0.273 Chirality : 0.038 0.153 1844 Planarity : 0.003 0.024 1888 Dihedral : 3.593 16.981 1652 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.11 (0.22), residues: 1516 helix: 2.61 (0.15), residues: 1104 sheet: 0.25 (0.65), residues: 96 loop : 0.74 (0.43), residues: 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2302 time to fit residues: 29.9688 Evaluate side-chains 54 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 10.0000 chunk 68 optimal weight: 50.0000 chunk 100 optimal weight: 0.1980 chunk 151 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 10960 Z= 0.135 Angle : 0.453 6.939 15036 Z= 0.258 Chirality : 0.038 0.164 1844 Planarity : 0.003 0.024 1888 Dihedral : 3.436 16.364 1652 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.30 (0.23), residues: 1516 helix: 2.74 (0.15), residues: 1108 sheet: 0.25 (0.65), residues: 96 loop : 0.80 (0.43), residues: 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2133 time to fit residues: 26.7009 Evaluate side-chains 57 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 8.9990 chunk 111 optimal weight: 50.0000 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 50.0000 chunk 120 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.053230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.042209 restraints weight = 100972.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042849 restraints weight = 76855.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.043386 restraints weight = 62369.591| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 10960 Z= 0.183 Angle : 0.494 6.933 15036 Z= 0.282 Chirality : 0.039 0.157 1844 Planarity : 0.003 0.023 1888 Dihedral : 3.537 16.793 1652 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.34 (0.23), residues: 1516 helix: 2.73 (0.15), residues: 1112 sheet: 0.07 (0.63), residues: 96 loop : 1.05 (0.45), residues: 308 =============================================================================== Job complete usr+sys time: 1626.09 seconds wall clock time: 30 minutes 34.27 seconds (1834.27 seconds total)