Starting phenix.real_space_refine on Fri Mar 15 05:53:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/03_2024/5v4s_8633.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/03_2024/5v4s_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_8633/03_2024/5v4s_8633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/03_2024/5v4s_8633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/03_2024/5v4s_8633.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8633/03_2024/5v4s_8633.pdb" } resolution = 4.2 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= 0.000 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 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. 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-5265/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: 6.23, per 1000 atoms: 0.58 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: 5.09 Conformation dependent library (CDL) restraints added in 2.3 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: 1.43 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: 3.80 Time building geometry restraints manager: 5.45 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 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: 0.540 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: 3.150 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 34.620 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 58 HIS 0.002 0.002 HIS D 161 PHE 0.011 0.002 PHE D 21 TYR 0.034 0.005 TYR A 272 ARG 0.003 0.001 ARG C 30 *********************** 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 : 1.184 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 REVERT: A 230 ASN cc_start: 0.8099 (m-40) cc_final: 0.7890 (t0) REVERT: C 230 ASN cc_start: 0.8120 (m-40) cc_final: 0.7902 (t0) REVERT: D 230 ASN cc_start: 0.8098 (m-40) cc_final: 0.7813 (t0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2861 time to fit residues: 58.2664 Evaluate side-chains 83 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.2440 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= 0.191 Angle : 0.529 6.868 15036 Z= 0.312 Chirality : 0.039 0.141 1844 Planarity : 0.005 0.065 1888 Dihedral : 4.050 15.275 1652 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.49 % Allowed : 2.80 % Favored : 96.71 % 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: 0.90 (0.21), residues: 1516 helix: 1.12 (0.15), residues: 1100 sheet: 0.34 (0.65), residues: 52 loop : -0.79 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 58 HIS 0.001 0.001 HIS B 161 PHE 0.019 0.002 PHE A 152 TYR 0.018 0.002 TYR A 272 ARG 0.003 0.001 ARG B 270 *********************** 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 122 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.210 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: A 230 ASN cc_start: 0.7721 (m-40) cc_final: 0.6963 (t0) REVERT: A 274 MET cc_start: 0.8180 (mtm) cc_final: 0.7913 (ptp) REVERT: B 274 MET cc_start: 0.8057 (mtm) cc_final: 0.7817 (ptp) REVERT: C 230 ASN cc_start: 0.7727 (m-40) cc_final: 0.7065 (t0) REVERT: C 274 MET cc_start: 0.8030 (mtm) cc_final: 0.7780 (ptp) REVERT: D 230 ASN cc_start: 0.7715 (m-40) cc_final: 0.6912 (t0) REVERT: D 274 MET cc_start: 0.8146 (mtm) cc_final: 0.7863 (ptp) outliers start: 4 outliers final: 0 residues processed: 122 average time/residue: 0.2692 time to fit residues: 44.4751 Evaluate side-chains 81 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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: 0.9990 chunk 114 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 50.0000 chunk 123 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN C 134 GLN D 59 ASN D 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10960 Z= 0.268 Angle : 0.570 6.148 15036 Z= 0.331 Chirality : 0.039 0.138 1844 Planarity : 0.005 0.045 1888 Dihedral : 4.014 15.291 1652 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 1.49 (0.21), residues: 1516 helix: 1.45 (0.15), residues: 1092 sheet: 0.93 (0.77), residues: 48 loop : -0.19 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 85 HIS 0.002 0.001 HIS A 161 PHE 0.025 0.002 PHE D 152 TYR 0.020 0.002 TYR A 272 ARG 0.019 0.001 ARG D 128 *********************** 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 100 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.396 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: A 249 MET cc_start: 0.6796 (mtp) cc_final: 0.6462 (tpp) REVERT: B 249 MET cc_start: 0.6768 (mtp) cc_final: 0.6397 (tpp) REVERT: C 249 MET cc_start: 0.6765 (mtp) cc_final: 0.6428 (tpp) REVERT: D 249 MET cc_start: 0.6758 (mtp) cc_final: 0.6419 (tpp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3245 time to fit residues: 42.5007 Evaluate side-chains 56 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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: 5.9990 chunk 103 optimal weight: 30.0000 chunk 71 optimal weight: 50.0000 chunk 15 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 146 optimal weight: 40.0000 chunk 72 optimal weight: 50.0000 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.6719 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10960 Z= 0.238 Angle : 0.534 6.050 15036 Z= 0.306 Chirality : 0.039 0.129 1844 Planarity : 0.004 0.042 1888 Dihedral : 3.995 16.134 1652 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 1.85 (0.21), residues: 1516 helix: 1.66 (0.15), residues: 1096 sheet: 1.53 (0.81), residues: 48 loop : 0.03 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 162 HIS 0.002 0.001 HIS B 161 PHE 0.019 0.002 PHE D 154 TYR 0.022 0.002 TYR B 272 ARG 0.011 0.001 ARG D 246 *********************** 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 84 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.277 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: A 274 MET cc_start: 0.8321 (mtm) cc_final: 0.7803 (ptp) REVERT: B 274 MET cc_start: 0.8299 (mtm) cc_final: 0.7791 (ptp) REVERT: C 274 MET cc_start: 0.8289 (mtm) cc_final: 0.7804 (ptp) REVERT: D 274 MET cc_start: 0.8241 (mtm) cc_final: 0.7786 (ptp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2723 time to fit residues: 31.4197 Evaluate side-chains 50 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 50.0000 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10960 Z= 0.220 Angle : 0.521 8.334 15036 Z= 0.295 Chirality : 0.038 0.130 1844 Planarity : 0.004 0.033 1888 Dihedral : 3.874 16.714 1652 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 2.31 (0.22), residues: 1516 helix: 1.93 (0.15), residues: 1096 sheet: 0.19 (0.59), residues: 96 loop : 0.79 (0.40), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 162 HIS 0.001 0.001 HIS A 161 PHE 0.028 0.002 PHE A 152 TYR 0.017 0.002 TYR D 272 ARG 0.003 0.000 ARG A 268 *********************** 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 72 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.198 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: A 274 MET cc_start: 0.8107 (mtm) cc_final: 0.7818 (ptp) REVERT: B 274 MET cc_start: 0.8139 (mtm) cc_final: 0.7791 (ptp) REVERT: C 274 MET cc_start: 0.8169 (mtm) cc_final: 0.7856 (ptp) REVERT: D 274 MET cc_start: 0.8196 (mtm) cc_final: 0.7858 (ptp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2634 time to fit residues: 26.5940 Evaluate side-chains 53 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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: 4.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 50.0000 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** B 161 HIS ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10960 Z= 0.147 Angle : 0.450 8.276 15036 Z= 0.260 Chirality : 0.037 0.139 1844 Planarity : 0.003 0.027 1888 Dihedral : 3.658 16.181 1652 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 2.69 (0.22), residues: 1516 helix: 2.24 (0.15), residues: 1104 sheet: 0.04 (0.64), residues: 88 loop : 0.80 (0.41), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 162 HIS 0.001 0.001 HIS B 161 PHE 0.025 0.002 PHE A 152 TYR 0.014 0.001 TYR B 272 ARG 0.002 0.000 ARG A 268 *********************** 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 83 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.208 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: A 274 MET cc_start: 0.7852 (mtm) cc_final: 0.7645 (ptp) REVERT: C 274 MET cc_start: 0.8052 (mtm) cc_final: 0.7789 (ptp) REVERT: D 274 MET cc_start: 0.8031 (mtm) cc_final: 0.7748 (ptp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2520 time to fit residues: 29.4705 Evaluate side-chains 54 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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: 30.0000 chunk 16 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 50.0000 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 146 optimal weight: 0.0770 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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 ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10960 Z= 0.166 Angle : 0.453 5.735 15036 Z= 0.263 Chirality : 0.038 0.146 1844 Planarity : 0.003 0.027 1888 Dihedral : 3.631 16.205 1652 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 2.75 (0.22), residues: 1516 helix: 2.30 (0.15), residues: 1108 sheet: -0.04 (0.66), residues: 88 loop : 0.78 (0.43), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 162 HIS 0.002 0.001 HIS B 161 PHE 0.019 0.002 PHE A 152 TYR 0.020 0.001 TYR B 272 ARG 0.003 0.000 ARG D 135 *********************** 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 88 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 274 MET cc_start: 0.7989 (mtm) cc_final: 0.7605 (ptp) REVERT: D 274 MET cc_start: 0.8017 (mtm) cc_final: 0.7621 (ptp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2289 time to fit residues: 29.2198 Evaluate side-chains 53 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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: 1.9990 chunk 87 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 72 optimal weight: 50.0000 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 0.3980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN C 141 GLN D 141 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10960 Z= 0.137 Angle : 0.455 7.856 15036 Z= 0.256 Chirality : 0.037 0.148 1844 Planarity : 0.003 0.026 1888 Dihedral : 3.521 15.652 1652 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 3.04 (0.22), residues: 1516 helix: 2.50 (0.15), residues: 1116 sheet: 0.16 (0.67), residues: 88 loop : 0.85 (0.43), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 162 HIS 0.001 0.000 HIS A 161 PHE 0.020 0.002 PHE D 152 TYR 0.017 0.001 TYR A 273 ARG 0.002 0.000 ARG B 268 *********************** 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 83 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.247 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: C 274 MET cc_start: 0.7829 (mtm) cc_final: 0.7589 (ptp) REVERT: D 274 MET cc_start: 0.7903 (mtm) cc_final: 0.7631 (ptp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2127 time to fit residues: 26.6024 Evaluate side-chains 53 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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: 5.9990 chunk 136 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 50.0000 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 144 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10960 Z= 0.254 Angle : 0.537 9.045 15036 Z= 0.309 Chirality : 0.039 0.149 1844 Planarity : 0.004 0.029 1888 Dihedral : 3.820 16.673 1652 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 3.01 (0.22), residues: 1516 helix: 2.46 (0.15), residues: 1100 sheet: 0.25 (0.64), residues: 96 loop : 1.04 (0.43), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 162 HIS 0.004 0.002 HIS B 161 PHE 0.018 0.002 PHE A 154 TYR 0.021 0.002 TYR A 272 ARG 0.003 0.000 ARG D 246 *********************** 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 76 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 MET cc_start: 0.7884 (mmm) cc_final: 0.7639 (mmm) REVERT: C 274 MET cc_start: 0.7907 (mtm) cc_final: 0.7662 (ptp) REVERT: D 274 MET cc_start: 0.8048 (mtm) cc_final: 0.7718 (ptp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2320 time to fit residues: 25.8011 Evaluate side-chains 54 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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: 7.9990 chunk 68 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10960 Z= 0.221 Angle : 0.527 9.245 15036 Z= 0.303 Chirality : 0.039 0.154 1844 Planarity : 0.003 0.026 1888 Dihedral : 3.888 17.707 1652 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 2.95 (0.22), residues: 1516 helix: 2.40 (0.15), residues: 1104 sheet: 0.17 (0.64), residues: 96 loop : 1.07 (0.42), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 162 HIS 0.002 0.001 HIS D 161 PHE 0.018 0.002 PHE D 154 TYR 0.020 0.002 TYR A 272 ARG 0.003 0.000 ARG B 268 ********************** 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 : 1.395 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: B 249 MET cc_start: 0.7892 (mmm) cc_final: 0.7598 (mmp) REVERT: C 274 MET cc_start: 0.7677 (mtm) cc_final: 0.7447 (ptp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2455 time to fit residues: 29.4747 Evaluate side-chains 55 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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: 6.9990 chunk 111 optimal weight: 50.0000 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 50.0000 chunk 120 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 124 optimal weight: 0.0970 chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 overall best weight: 3.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 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 = 0.3317 r_free = 0.3317 target = 0.051371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040745 restraints weight = 109209.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.041336 restraints weight = 82580.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.041709 restraints weight = 67059.933| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10960 Z= 0.199 Angle : 0.509 9.269 15036 Z= 0.291 Chirality : 0.039 0.152 1844 Planarity : 0.003 0.026 1888 Dihedral : 3.837 17.238 1652 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 2.97 (0.22), residues: 1516 helix: 2.41 (0.15), residues: 1104 sheet: 0.13 (0.63), residues: 96 loop : 1.08 (0.43), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 162 HIS 0.002 0.001 HIS B 161 PHE 0.019 0.002 PHE D 154 TYR 0.021 0.002 TYR D 272 ARG 0.002 0.000 ARG D 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.43 seconds wall clock time: 31 minutes 59.27 seconds (1919.27 seconds total)