Starting phenix.real_space_refine on Thu Feb 15 01:35:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8632/02_2024/5v4s_8632.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8632/02_2024/5v4s_8632.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_8632/02_2024/5v4s_8632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8632/02_2024/5v4s_8632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8632/02_2024/5v4s_8632.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v4s_8632/02_2024/5v4s_8632.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= 0.001 sd= 0.009 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-5238/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: 6.36, per 1000 atoms: 0.59 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: 5.28 Conformation dependent library (CDL) restraints added in 2.2 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: 1.28 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: 5.36 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: 0.010 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: 3.180 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.510 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 403 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8582 (t) cc_final: 0.8307 (t) REVERT: A 30 ARG cc_start: 0.7106 (mtt180) cc_final: 0.5941 (mmp80) REVERT: A 88 ILE cc_start: 0.8451 (mt) cc_final: 0.8148 (mm) REVERT: A 134 GLN cc_start: 0.8432 (tp40) cc_final: 0.8110 (tp40) REVERT: A 249 MET cc_start: 0.8463 (ttp) cc_final: 0.8247 (ttm) REVERT: B 10 VAL cc_start: 0.8571 (t) cc_final: 0.8288 (t) REVERT: B 30 ARG cc_start: 0.7114 (mtt180) cc_final: 0.5910 (mmp80) REVERT: B 88 ILE cc_start: 0.8460 (mt) cc_final: 0.8151 (mm) REVERT: B 134 GLN cc_start: 0.8435 (tp40) cc_final: 0.8127 (tp40) REVERT: B 249 MET cc_start: 0.8498 (ttp) cc_final: 0.8269 (ttm) REVERT: C 10 VAL cc_start: 0.8563 (t) cc_final: 0.8280 (t) REVERT: C 30 ARG cc_start: 0.7134 (mtt180) cc_final: 0.5893 (mmp80) REVERT: C 88 ILE cc_start: 0.8455 (mt) cc_final: 0.8158 (mm) REVERT: C 134 GLN cc_start: 0.8382 (tp40) cc_final: 0.8052 (tp40) REVERT: C 249 MET cc_start: 0.8501 (ttp) cc_final: 0.8282 (ttm) REVERT: D 10 VAL cc_start: 0.8553 (t) cc_final: 0.8264 (t) REVERT: D 30 ARG cc_start: 0.7137 (mtt180) cc_final: 0.5934 (mmp80) REVERT: D 88 ILE cc_start: 0.8445 (mt) cc_final: 0.8155 (mm) REVERT: D 134 GLN cc_start: 0.8384 (tp40) cc_final: 0.8054 (tp40) REVERT: D 249 MET cc_start: 0.8448 (ttp) cc_final: 0.8241 (ttm) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.2762 time to fit residues: 146.2963 Evaluate side-chains 189 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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: 0.4980 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7364 moved from start: 0.3678 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= 0.199 Angle : 0.532 7.253 15036 Z= 0.301 Chirality : 0.038 0.130 1844 Planarity : 0.005 0.068 1888 Dihedral : 4.194 16.810 1652 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: 1.18 (0.21), residues: 1516 helix: 1.49 (0.15), residues: 1072 sheet: 0.18 (0.65), residues: 52 loop : -1.06 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 85 HIS 0.003 0.002 HIS B 161 PHE 0.011 0.001 PHE C 21 TYR 0.018 0.002 TYR C 272 ARG 0.010 0.001 ARG A 9 *********************** 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 278 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.219 Fit side-chains REVERT: A 10 VAL cc_start: 0.8609 (t) cc_final: 0.8367 (t) REVERT: A 28 PRO cc_start: 0.9019 (Cg_endo) cc_final: 0.8811 (Cg_exo) REVERT: A 134 GLN cc_start: 0.8472 (tp40) cc_final: 0.7720 (tp-100) REVERT: A 249 MET cc_start: 0.8826 (ttp) cc_final: 0.8436 (ttm) REVERT: B 134 GLN cc_start: 0.8472 (tp40) cc_final: 0.7782 (tp-100) REVERT: B 249 MET cc_start: 0.8911 (ttp) cc_final: 0.8428 (ttm) REVERT: C 134 GLN cc_start: 0.8413 (tp40) cc_final: 0.7711 (tp-100) REVERT: C 162 TRP cc_start: 0.8784 (m-10) cc_final: 0.8077 (m100) REVERT: C 249 MET cc_start: 0.8886 (ttp) cc_final: 0.8289 (ttm) REVERT: D 10 VAL cc_start: 0.8643 (t) cc_final: 0.8404 (t) REVERT: D 28 PRO cc_start: 0.9052 (Cg_endo) cc_final: 0.8841 (Cg_exo) REVERT: D 134 GLN cc_start: 0.8458 (tp40) cc_final: 0.7751 (tp-100) REVERT: D 249 MET cc_start: 0.8802 (ttp) cc_final: 0.8412 (ttm) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2539 time to fit residues: 95.3703 Evaluate side-chains 160 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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: 9.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 chunk 123 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 10960 Z= 0.498 Angle : 0.754 9.315 15036 Z= 0.407 Chirality : 0.046 0.180 1844 Planarity : 0.005 0.055 1888 Dihedral : 4.557 19.824 1652 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % 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: 0.49 (0.21), residues: 1516 helix: 0.91 (0.15), residues: 1076 sheet: 0.17 (0.75), residues: 48 loop : -1.14 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 155 HIS 0.008 0.005 HIS B 161 PHE 0.033 0.004 PHE A 47 TYR 0.033 0.003 TYR C 45 ARG 0.026 0.001 ARG A 135 *********************** 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 188 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.258 Fit side-chains REVERT: A 41 LEU cc_start: 0.7623 (mm) cc_final: 0.7289 (pt) REVERT: A 138 LEU cc_start: 0.8786 (mt) cc_final: 0.8391 (mt) REVERT: A 249 MET cc_start: 0.9002 (ttp) cc_final: 0.8393 (ttm) REVERT: A 253 ASP cc_start: 0.8007 (m-30) cc_final: 0.7756 (m-30) REVERT: B 7 ARG cc_start: 0.4078 (mtp180) cc_final: 0.3310 (ttm110) REVERT: B 41 LEU cc_start: 0.7724 (mm) cc_final: 0.7369 (pt) REVERT: C 7 ARG cc_start: 0.4151 (mtp180) cc_final: 0.3357 (ttm110) REVERT: C 41 LEU cc_start: 0.7807 (mm) cc_final: 0.7457 (pt) REVERT: D 7 ARG cc_start: 0.3990 (mtp180) cc_final: 0.3174 (ttm110) REVERT: D 41 LEU cc_start: 0.7731 (mm) cc_final: 0.7395 (pt) REVERT: D 249 MET cc_start: 0.9004 (ttp) cc_final: 0.8390 (ttm) REVERT: D 253 ASP cc_start: 0.8016 (m-30) cc_final: 0.7768 (m-30) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2434 time to fit residues: 64.1587 Evaluate side-chains 137 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 146 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 chunk 131 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN B 134 GLN B 141 GLN B 230 ASN C 134 GLN C 230 ASN D 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5335 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= 0.193 Angle : 0.491 6.577 15036 Z= 0.268 Chirality : 0.037 0.123 1844 Planarity : 0.004 0.067 1888 Dihedral : 3.861 16.142 1652 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.37 % Allowed : 2.44 % Favored : 97.20 % 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: 1.62 (0.21), residues: 1516 helix: 1.75 (0.15), residues: 1092 sheet: -0.30 (0.59), residues: 88 loop : -0.70 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 85 HIS 0.003 0.002 HIS D 161 PHE 0.017 0.002 PHE A 154 TYR 0.011 0.001 TYR A 169 ARG 0.010 0.001 ARG A 135 *********************** 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 221 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 218 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.7677 (mm) cc_final: 0.7411 (pt) REVERT: A 89 ASP cc_start: 0.7637 (m-30) cc_final: 0.7290 (t0) REVERT: A 134 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7808 (tp40) REVERT: A 162 TRP cc_start: 0.8467 (m-10) cc_final: 0.8131 (m100) REVERT: A 249 MET cc_start: 0.8914 (ttp) cc_final: 0.8109 (ttm) REVERT: A 253 ASP cc_start: 0.8142 (m-30) cc_final: 0.7835 (m-30) REVERT: B 41 LEU cc_start: 0.7697 (mm) cc_final: 0.7409 (pt) REVERT: B 89 ASP cc_start: 0.7535 (m-30) cc_final: 0.7239 (t0) REVERT: B 134 GLN cc_start: 0.8462 (tp-100) cc_final: 0.7868 (tp40) REVERT: B 162 TRP cc_start: 0.8457 (m-10) cc_final: 0.8129 (m100) REVERT: B 249 MET cc_start: 0.8548 (ttm) cc_final: 0.7945 (ttm) REVERT: B 253 ASP cc_start: 0.8110 (m-30) cc_final: 0.7853 (m-30) REVERT: B 274 MET cc_start: 0.8598 (mmm) cc_final: 0.8200 (mmm) REVERT: C 41 LEU cc_start: 0.7661 (mm) cc_final: 0.7381 (pt) REVERT: C 89 ASP cc_start: 0.7662 (m-30) cc_final: 0.7327 (t0) REVERT: C 134 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7941 (tp40) REVERT: C 162 TRP cc_start: 0.8472 (m-10) cc_final: 0.8129 (m100) REVERT: C 249 MET cc_start: 0.8583 (ttm) cc_final: 0.8052 (ttm) REVERT: C 253 ASP cc_start: 0.8194 (m-30) cc_final: 0.7883 (m-30) REVERT: C 274 MET cc_start: 0.8663 (mmm) cc_final: 0.8394 (mmm) REVERT: D 7 ARG cc_start: 0.3937 (mtp180) cc_final: 0.3239 (ttm110) REVERT: D 41 LEU cc_start: 0.7659 (mm) cc_final: 0.7407 (pt) REVERT: D 89 ASP cc_start: 0.7546 (m-30) cc_final: 0.7258 (t0) REVERT: D 134 GLN cc_start: 0.8301 (tp40) cc_final: 0.7642 (tp40) REVERT: D 162 TRP cc_start: 0.8471 (m-10) cc_final: 0.8136 (m100) outliers start: 3 outliers final: 0 residues processed: 221 average time/residue: 0.2290 time to fit residues: 71.2183 Evaluate side-chains 182 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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: 0.8980 chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 0.0060 chunk 109 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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: 0.7450 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10960 Z= 0.162 Angle : 0.442 6.342 15036 Z= 0.247 Chirality : 0.036 0.122 1844 Planarity : 0.003 0.042 1888 Dihedral : 3.574 15.784 1652 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 2.18 (0.21), residues: 1516 helix: 2.17 (0.14), residues: 1092 sheet: -0.31 (0.60), residues: 88 loop : -0.46 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 189 HIS 0.002 0.001 HIS D 161 PHE 0.017 0.001 PHE A 154 TYR 0.012 0.001 TYR D 169 ARG 0.005 0.000 ARG B 135 *********************** 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 213 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8786 (t) cc_final: 0.8502 (t) REVERT: A 41 LEU cc_start: 0.7816 (mm) cc_final: 0.7475 (pt) REVERT: A 162 TRP cc_start: 0.8404 (m-10) cc_final: 0.8134 (m100) REVERT: B 41 LEU cc_start: 0.7845 (mm) cc_final: 0.7482 (pt) REVERT: B 97 GLU cc_start: 0.7358 (pm20) cc_final: 0.7094 (mm-30) REVERT: B 98 TYR cc_start: 0.6386 (t80) cc_final: 0.6137 (t80) REVERT: B 162 TRP cc_start: 0.8449 (m-10) cc_final: 0.8138 (m100) REVERT: B 274 MET cc_start: 0.8583 (mmm) cc_final: 0.8133 (mmm) REVERT: C 41 LEU cc_start: 0.7905 (mm) cc_final: 0.7578 (pt) REVERT: C 49 ASP cc_start: 0.6815 (p0) cc_final: 0.6590 (m-30) REVERT: C 89 ASP cc_start: 0.7623 (m-30) cc_final: 0.7273 (t0) REVERT: C 125 LYS cc_start: 0.8676 (tttp) cc_final: 0.8103 (tttp) REVERT: C 134 GLN cc_start: 0.8461 (tp-100) cc_final: 0.8229 (tp-100) REVERT: C 162 TRP cc_start: 0.8407 (m-10) cc_final: 0.8126 (m100) REVERT: C 274 MET cc_start: 0.8641 (mmm) cc_final: 0.8263 (mmm) REVERT: D 7 ARG cc_start: 0.3710 (mtp180) cc_final: 0.3501 (ttm170) REVERT: D 41 LEU cc_start: 0.7876 (mm) cc_final: 0.7570 (pt) REVERT: D 125 LYS cc_start: 0.8832 (tttp) cc_final: 0.8439 (tttp) REVERT: D 134 GLN cc_start: 0.8337 (tp40) cc_final: 0.7825 (tp-100) REVERT: D 162 TRP cc_start: 0.8413 (m-10) cc_final: 0.8135 (m100) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2132 time to fit residues: 65.4884 Evaluate side-chains 159 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.6036 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= 0.210 Angle : 0.472 6.602 15036 Z= 0.258 Chirality : 0.037 0.121 1844 Planarity : 0.003 0.040 1888 Dihedral : 3.520 16.119 1652 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 2.42 (0.21), residues: 1516 helix: 2.36 (0.14), residues: 1092 sheet: -0.36 (0.59), residues: 88 loop : -0.40 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 12 HIS 0.004 0.002 HIS A 161 PHE 0.021 0.002 PHE B 154 TYR 0.013 0.002 TYR C 188 ARG 0.004 0.000 ARG B 135 *********************** 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 198 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8611 (t) cc_final: 0.8356 (t) REVERT: A 41 LEU cc_start: 0.7865 (mm) cc_final: 0.7469 (pt) REVERT: A 134 GLN cc_start: 0.8356 (tm130) cc_final: 0.7687 (tp40) REVERT: A 162 TRP cc_start: 0.8447 (m-10) cc_final: 0.8165 (m100) REVERT: A 249 MET cc_start: 0.8567 (ttm) cc_final: 0.7956 (ttm) REVERT: A 253 ASP cc_start: 0.8324 (m-30) cc_final: 0.8052 (m-30) REVERT: B 41 LEU cc_start: 0.7947 (mm) cc_final: 0.7514 (pt) REVERT: B 98 TYR cc_start: 0.6165 (t80) cc_final: 0.5837 (t80) REVERT: B 134 GLN cc_start: 0.8113 (tp40) cc_final: 0.7710 (tp40) REVERT: C 41 LEU cc_start: 0.7860 (mm) cc_final: 0.7509 (pt) REVERT: C 134 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7604 (tp-100) REVERT: C 162 TRP cc_start: 0.8469 (m-10) cc_final: 0.8173 (m100) REVERT: C 274 MET cc_start: 0.8636 (mmm) cc_final: 0.8338 (mmm) REVERT: D 7 ARG cc_start: 0.3998 (mtp180) cc_final: 0.3728 (ttm170) REVERT: D 41 LEU cc_start: 0.7876 (mm) cc_final: 0.7537 (pt) REVERT: D 134 GLN cc_start: 0.8398 (tp40) cc_final: 0.7880 (tp-100) REVERT: D 138 LEU cc_start: 0.8875 (mt) cc_final: 0.8580 (mt) REVERT: D 162 TRP cc_start: 0.8441 (m-10) cc_final: 0.8168 (m100) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2146 time to fit residues: 61.9489 Evaluate side-chains 171 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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: 0.0010 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.0010 chunk 107 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10960 Z= 0.204 Angle : 0.470 6.409 15036 Z= 0.257 Chirality : 0.037 0.121 1844 Planarity : 0.004 0.050 1888 Dihedral : 3.509 16.464 1652 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 2.50 (0.21), residues: 1516 helix: 2.36 (0.14), residues: 1096 sheet: -0.31 (0.61), residues: 88 loop : -0.15 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 12 HIS 0.003 0.002 HIS A 161 PHE 0.021 0.002 PHE A 154 TYR 0.011 0.001 TYR C 188 ARG 0.004 0.000 ARG A 270 *********************** 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 198 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8588 (t) cc_final: 0.8303 (t) REVERT: A 41 LEU cc_start: 0.7864 (mm) cc_final: 0.7533 (pt) REVERT: A 97 GLU cc_start: 0.7432 (pm20) cc_final: 0.7155 (mm-30) REVERT: A 134 GLN cc_start: 0.8478 (tm130) cc_final: 0.7718 (tp40) REVERT: A 162 TRP cc_start: 0.8365 (m-10) cc_final: 0.8137 (m100) REVERT: A 249 MET cc_start: 0.8745 (ttm) cc_final: 0.8267 (ttm) REVERT: A 253 ASP cc_start: 0.8341 (m-30) cc_final: 0.8077 (m-30) REVERT: B 7 ARG cc_start: 0.3803 (mtp180) cc_final: 0.3298 (ttm110) REVERT: B 41 LEU cc_start: 0.7974 (mm) cc_final: 0.7549 (pt) REVERT: B 134 GLN cc_start: 0.8056 (tp40) cc_final: 0.7544 (tp-100) REVERT: B 162 TRP cc_start: 0.8370 (m-10) cc_final: 0.8060 (m100) REVERT: B 165 VAL cc_start: 0.9324 (t) cc_final: 0.9046 (p) REVERT: C 7 ARG cc_start: 0.3827 (mtp180) cc_final: 0.3310 (ttm110) REVERT: C 41 LEU cc_start: 0.7991 (mm) cc_final: 0.7639 (pt) REVERT: C 97 GLU cc_start: 0.7465 (pm20) cc_final: 0.7141 (mm-30) REVERT: C 134 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7655 (tp-100) REVERT: C 138 LEU cc_start: 0.8926 (pp) cc_final: 0.8723 (pp) REVERT: C 162 TRP cc_start: 0.8390 (m-10) cc_final: 0.8159 (m100) REVERT: D 7 ARG cc_start: 0.4034 (mtp180) cc_final: 0.3497 (ttm110) REVERT: D 41 LEU cc_start: 0.7895 (mm) cc_final: 0.7527 (pt) REVERT: D 97 GLU cc_start: 0.7460 (pm20) cc_final: 0.7212 (mm-30) REVERT: D 162 TRP cc_start: 0.8385 (m-10) cc_final: 0.8077 (m100) REVERT: D 165 VAL cc_start: 0.9308 (t) cc_final: 0.9030 (p) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2183 time to fit residues: 62.1667 Evaluate side-chains 154 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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: 0.9990 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 chunk 72 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10960 Z= 0.172 Angle : 0.464 7.932 15036 Z= 0.248 Chirality : 0.037 0.120 1844 Planarity : 0.003 0.039 1888 Dihedral : 3.385 15.943 1652 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: 2.79 (0.21), residues: 1516 helix: 2.55 (0.14), residues: 1096 sheet: -0.12 (0.63), residues: 88 loop : 0.01 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 58 HIS 0.002 0.001 HIS C 161 PHE 0.016 0.001 PHE D 154 TYR 0.011 0.001 TYR A 169 ARG 0.004 0.000 ARG A 135 *********************** 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 206 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8597 (t) cc_final: 0.8302 (t) REVERT: A 41 LEU cc_start: 0.7874 (mm) cc_final: 0.7558 (pt) REVERT: A 97 GLU cc_start: 0.7372 (pm20) cc_final: 0.7077 (mm-30) REVERT: A 134 GLN cc_start: 0.8442 (tm130) cc_final: 0.7654 (tp40) REVERT: A 137 ASN cc_start: 0.8012 (t0) cc_final: 0.7652 (t0) REVERT: A 162 TRP cc_start: 0.8341 (m-10) cc_final: 0.8055 (m100) REVERT: A 165 VAL cc_start: 0.9306 (t) cc_final: 0.9046 (p) REVERT: A 249 MET cc_start: 0.8586 (ttm) cc_final: 0.7963 (ttm) REVERT: A 253 ASP cc_start: 0.8370 (m-30) cc_final: 0.8040 (m-30) REVERT: B 7 ARG cc_start: 0.3760 (mtp180) cc_final: 0.3305 (ttm110) REVERT: B 41 LEU cc_start: 0.7937 (mm) cc_final: 0.7554 (pt) REVERT: B 134 GLN cc_start: 0.8078 (tp40) cc_final: 0.7427 (tp40) REVERT: B 138 LEU cc_start: 0.9016 (pp) cc_final: 0.8628 (pp) REVERT: B 162 TRP cc_start: 0.8387 (m-10) cc_final: 0.8071 (m100) REVERT: B 165 VAL cc_start: 0.9283 (t) cc_final: 0.9017 (p) REVERT: C 7 ARG cc_start: 0.3685 (mtp180) cc_final: 0.3251 (ttm110) REVERT: C 41 LEU cc_start: 0.7993 (mm) cc_final: 0.7388 (pt) REVERT: C 97 GLU cc_start: 0.7390 (pm20) cc_final: 0.7077 (mm-30) REVERT: C 134 GLN cc_start: 0.8310 (tp-100) cc_final: 0.7686 (tp-100) REVERT: C 162 TRP cc_start: 0.8348 (m-10) cc_final: 0.8087 (m100) REVERT: C 165 VAL cc_start: 0.9248 (t) cc_final: 0.9019 (p) REVERT: D 7 ARG cc_start: 0.4059 (mtp180) cc_final: 0.3518 (ttm110) REVERT: D 41 LEU cc_start: 0.8007 (mm) cc_final: 0.7426 (pt) REVERT: D 97 GLU cc_start: 0.7399 (pm20) cc_final: 0.7127 (mm-30) REVERT: D 162 TRP cc_start: 0.8341 (m-10) cc_final: 0.8082 (m100) REVERT: D 165 VAL cc_start: 0.9257 (t) cc_final: 0.9022 (p) REVERT: D 274 MET cc_start: 0.8607 (mmm) cc_final: 0.8389 (mmm) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1932 time to fit residues: 58.6604 Evaluate side-chains 182 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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: 1.9990 chunk 136 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 50.0000 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 40.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10960 Z= 0.217 Angle : 0.497 6.601 15036 Z= 0.268 Chirality : 0.037 0.120 1844 Planarity : 0.003 0.039 1888 Dihedral : 3.437 15.329 1652 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.70 (0.22), residues: 1516 helix: 2.48 (0.14), residues: 1096 sheet: -0.08 (0.63), residues: 88 loop : -0.02 (0.38), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 58 HIS 0.004 0.002 HIS A 161 PHE 0.016 0.002 PHE A 154 TYR 0.013 0.002 TYR D 273 ARG 0.002 0.000 ARG B 135 *********************** 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 206 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8707 (t) cc_final: 0.8460 (t) REVERT: A 41 LEU cc_start: 0.7895 (mm) cc_final: 0.7560 (pt) REVERT: A 249 MET cc_start: 0.8700 (ttm) cc_final: 0.8157 (ttm) REVERT: A 253 ASP cc_start: 0.8301 (m-30) cc_final: 0.8026 (m-30) REVERT: B 7 ARG cc_start: 0.4031 (mtp180) cc_final: 0.3379 (ttm110) REVERT: B 41 LEU cc_start: 0.7984 (mm) cc_final: 0.7546 (pt) REVERT: B 134 GLN cc_start: 0.8129 (tp40) cc_final: 0.7453 (tp40) REVERT: B 138 LEU cc_start: 0.9078 (pp) cc_final: 0.8696 (pp) REVERT: C 7 ARG cc_start: 0.4072 (mtp180) cc_final: 0.3411 (ttm110) REVERT: C 134 GLN cc_start: 0.8357 (tp-100) cc_final: 0.7708 (tp-100) REVERT: D 7 ARG cc_start: 0.4101 (mtp180) cc_final: 0.3593 (ttm110) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1659 time to fit residues: 50.3237 Evaluate side-chains 155 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 40.0000 chunk 100 optimal weight: 0.0030 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 73 optimal weight: 50.0000 chunk 95 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10960 Z= 0.157 Angle : 0.478 8.569 15036 Z= 0.251 Chirality : 0.037 0.119 1844 Planarity : 0.003 0.039 1888 Dihedral : 3.311 14.071 1652 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 2.93 (0.22), residues: 1516 helix: 2.64 (0.15), residues: 1096 sheet: 0.09 (0.64), residues: 88 loop : 0.08 (0.38), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 22 HIS 0.002 0.001 HIS D 161 PHE 0.016 0.001 PHE C 154 TYR 0.010 0.001 TYR D 169 ARG 0.013 0.000 ARG A 135 ********************** 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 218 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.137 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 10 VAL cc_start: 0.8752 (t) cc_final: 0.8522 (t) REVERT: A 41 LEU cc_start: 0.7944 (mm) cc_final: 0.7690 (pt) REVERT: A 134 GLN cc_start: 0.8535 (tm130) cc_final: 0.7527 (tp40) REVERT: A 162 TRP cc_start: 0.8304 (m-10) cc_final: 0.8051 (m100) REVERT: A 249 MET cc_start: 0.8553 (ttm) cc_final: 0.8103 (ttm) REVERT: A 253 ASP cc_start: 0.8281 (m-30) cc_final: 0.7979 (m-30) REVERT: B 7 ARG cc_start: 0.3992 (mtp180) cc_final: 0.3363 (ttm110) REVERT: B 41 LEU cc_start: 0.7979 (mm) cc_final: 0.7683 (pt) REVERT: B 134 GLN cc_start: 0.8129 (tp40) cc_final: 0.7778 (tp40) REVERT: B 162 TRP cc_start: 0.8378 (m-10) cc_final: 0.8070 (m100) REVERT: B 165 VAL cc_start: 0.9230 (t) cc_final: 0.9005 (p) REVERT: C 7 ARG cc_start: 0.3988 (mtp180) cc_final: 0.3398 (ttm110) REVERT: C 134 GLN cc_start: 0.8376 (tp-100) cc_final: 0.7739 (tp-100) REVERT: C 162 TRP cc_start: 0.8375 (m-10) cc_final: 0.8073 (m100) REVERT: C 165 VAL cc_start: 0.9216 (t) cc_final: 0.8999 (p) REVERT: C 249 MET cc_start: 0.8235 (tpp) cc_final: 0.7963 (ttm) REVERT: D 7 ARG cc_start: 0.4151 (mtp180) cc_final: 0.3637 (ttm170) REVERT: D 89 ASP cc_start: 0.7876 (t70) cc_final: 0.7154 (t70) REVERT: D 162 TRP cc_start: 0.8392 (m-10) cc_final: 0.8073 (m100) REVERT: D 165 VAL cc_start: 0.9234 (t) cc_final: 0.9000 (p) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1996 time to fit residues: 62.4670 Evaluate side-chains 174 residues out of total 1348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 30.0000 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 40.0000 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 30.0000 chunk 6 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.175596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135239 restraints weight = 22390.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 92)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117899 restraints weight = 32050.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116631 restraints weight = 33576.503| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10960 Z= 0.224 Angle : 0.522 8.017 15036 Z= 0.276 Chirality : 0.037 0.119 1844 Planarity : 0.004 0.075 1888 Dihedral : 3.424 14.617 1652 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.83 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: 2.72 (0.22), residues: 1516 helix: 2.50 (0.15), residues: 1096 sheet: -0.12 (0.62), residues: 88 loop : -0.04 (0.38), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 58 HIS 0.004 0.002 HIS A 161 PHE 0.015 0.002 PHE A 154 TYR 0.013 0.002 TYR C 273 ARG 0.017 0.001 ARG A 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.96 seconds wall clock time: 41 minutes 52.84 seconds (2512.84 seconds total)