Starting phenix.real_space_refine on Mon Mar 11 06:53:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv6_36669/03_2024/8jv6_36669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv6_36669/03_2024/8jv6_36669.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv6_36669/03_2024/8jv6_36669_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv6_36669/03_2024/8jv6_36669_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv6_36669/03_2024/8jv6_36669_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv6_36669/03_2024/8jv6_36669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv6_36669/03_2024/8jv6_36669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv6_36669/03_2024/8jv6_36669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jv6_36669/03_2024/8jv6_36669_updated.pdb" } resolution = 3.43 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= 0.160 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 Cl 3 4.86 5 C 4704 2.51 5 N 1254 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ASP 265": "OD1" <-> "OD2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7458 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2402 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 297} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2402 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 297} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2402 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 297} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'NAG': 3, 'P6E': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {'NAG': 5, 'P6E': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {'NAG': 4, 'P6E': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.78, per 1000 atoms: 0.64 Number of scatterers: 7458 At special positions: 0 Unit cell: (89.89, 86.33, 113.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 48 16.00 O 1449 8.00 N 1254 7.00 C 4704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 264 " - pdb=" SG CYS C 273 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 403 " - " ASN A 187 " " NAG B 405 " - " ASN B 187 " " NAG C 404 " - " ASN C 187 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 21 sheets defined 19.8% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 235 through 242 removed outlier: 3.823A pdb=" N ALA A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.138A pdb=" N VAL A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.643A pdb=" N GLY A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 235 through 242 removed outlier: 3.747A pdb=" N ALA B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.095A pdb=" N VAL B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 335 through 357 removed outlier: 3.676A pdb=" N GLY B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 89 through 92 No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 235 through 242 removed outlier: 3.736A pdb=" N ALA C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 4.009A pdb=" N VAL C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 335 through 357 removed outlier: 3.661A pdb=" N GLY C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 58 through 61 Processing sheet with id= B, first strand: chain 'A' and resid 64 through 72 Processing sheet with id= C, first strand: chain 'A' and resid 75 through 79 removed outlier: 3.502A pdb=" N ALA A 75 " --> pdb=" O TRP A 87 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 115 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 195 through 198 Processing sheet with id= F, first strand: chain 'A' and resid 276 through 281 removed outlier: 6.085A pdb=" N ILE A 320 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU A 105 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE A 322 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE A 103 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 324 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N SER A 101 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 296 through 304 Processing sheet with id= H, first strand: chain 'B' and resid 58 through 61 Processing sheet with id= I, first strand: chain 'B' and resid 64 through 72 Processing sheet with id= J, first strand: chain 'B' and resid 75 through 79 removed outlier: 3.501A pdb=" N ALA B 75 " --> pdb=" O TRP B 87 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 115 through 119 Processing sheet with id= L, first strand: chain 'B' and resid 195 through 198 Processing sheet with id= M, first strand: chain 'B' and resid 276 through 281 removed outlier: 6.117A pdb=" N ILE B 320 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU B 105 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE B 322 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE B 103 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL B 324 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER B 101 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 296 through 304 Processing sheet with id= O, first strand: chain 'C' and resid 58 through 61 Processing sheet with id= P, first strand: chain 'C' and resid 64 through 72 Processing sheet with id= Q, first strand: chain 'C' and resid 75 through 79 Processing sheet with id= R, first strand: chain 'C' and resid 115 through 119 Processing sheet with id= S, first strand: chain 'C' and resid 195 through 198 Processing sheet with id= T, first strand: chain 'C' and resid 276 through 281 removed outlier: 6.348A pdb=" N ILE C 320 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU C 105 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE C 322 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE C 103 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C 324 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N SER C 101 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 296 through 304 274 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1239 1.31 - 1.43: 2073 1.43 - 1.56: 4241 1.56 - 1.69: 1 1.69 - 1.82: 69 Bond restraints: 7623 Sorted by residual: bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.09e+00 bond pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 2.05e+00 bond pdb=" C1 NAG B 405 " pdb=" O5 NAG B 405 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" C1 NAG A 403 " pdb=" O5 NAG A 403 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 7618 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 269 107.08 - 113.81: 4217 113.81 - 120.54: 2871 120.54 - 127.27: 2970 127.27 - 133.99: 71 Bond angle restraints: 10398 Sorted by residual: angle pdb=" CB MET A 256 " pdb=" CG MET A 256 " pdb=" SD MET A 256 " ideal model delta sigma weight residual 112.70 120.50 -7.80 3.00e+00 1.11e-01 6.75e+00 angle pdb=" CA PRO A 210 " pdb=" N PRO A 210 " pdb=" CD PRO A 210 " ideal model delta sigma weight residual 112.00 108.65 3.35 1.40e+00 5.10e-01 5.73e+00 angle pdb=" C LYS B 118 " pdb=" N CYS B 119 " pdb=" CA CYS B 119 " ideal model delta sigma weight residual 121.80 117.78 4.02 1.71e+00 3.42e-01 5.52e+00 angle pdb=" C LYS A 118 " pdb=" N CYS A 119 " pdb=" CA CYS A 119 " ideal model delta sigma weight residual 121.80 117.84 3.96 1.71e+00 3.42e-01 5.36e+00 angle pdb=" CA CYS A 119 " pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " ideal model delta sigma weight residual 114.40 119.06 -4.66 2.30e+00 1.89e-01 4.11e+00 ... (remaining 10393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 4130 18.08 - 36.15: 418 36.15 - 54.23: 117 54.23 - 72.30: 21 72.30 - 90.38: 12 Dihedral angle restraints: 4698 sinusoidal: 1959 harmonic: 2739 Sorted by residual: dihedral pdb=" CB CYS C 220 " pdb=" SG CYS C 220 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual 93.00 -176.62 -90.38 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual 93.00 -176.64 -90.36 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS B 220 " pdb=" SG CYS B 220 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual 93.00 -176.73 -90.27 1 1.00e+01 1.00e-02 9.65e+01 ... (remaining 4695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 739 0.033 - 0.067: 266 0.067 - 0.100: 127 0.100 - 0.133: 49 0.133 - 0.167: 4 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CB ILE C 173 " pdb=" CA ILE C 173 " pdb=" CG1 ILE C 173 " pdb=" CG2 ILE C 173 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ILE A 320 " pdb=" N ILE A 320 " pdb=" C ILE A 320 " pdb=" CB ILE A 320 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1182 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 122 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO C 123 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 209 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO A 210 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 286 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 287 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.021 5.00e-02 4.00e+02 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 361 2.73 - 3.27: 7081 3.27 - 3.81: 11565 3.81 - 4.36: 13554 4.36 - 4.90: 24553 Nonbonded interactions: 57114 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OD1 ASP C 91 " model vdw 2.184 2.440 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR B 302 " model vdw 2.186 2.440 nonbonded pdb=" OD1 ASP B 91 " pdb=" OH TYR C 302 " model vdw 2.199 2.440 nonbonded pdb=" O ASP C 145 " pdb=" OG SER C 166 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR A 130 " pdb=" OD2 ASP A 134 " model vdw 2.288 2.440 ... (remaining 57109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 358 or resid 401 through 403)) selection = (chain 'B' and (resid 43 through 358 or resid 401 through 403)) selection = (chain 'C' and (resid 43 through 358 or resid 401 through 403)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 3.880 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.350 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 7623 Z= 0.252 Angle : 0.595 7.796 10398 Z= 0.308 Chirality : 0.045 0.167 1185 Planarity : 0.005 0.075 1350 Dihedral : 15.645 89.805 2895 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.26 (0.27), residues: 942 helix: 0.61 (0.40), residues: 198 sheet: 0.76 (0.27), residues: 318 loop : -0.41 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 167 HIS 0.001 0.000 HIS A 132 PHE 0.011 0.001 PHE A 299 TYR 0.016 0.001 TYR A 53 ARG 0.009 0.001 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.889 Fit side-chains REVERT: C 267 ASP cc_start: 0.7166 (m-30) cc_final: 0.6606 (m-30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2321 time to fit residues: 23.0930 Evaluate side-chains 72 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.5980 chunk 70 optimal weight: 40.0000 chunk 39 optimal weight: 50.0000 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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: 0.7941 moved from start: 0.0379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7623 Z= 0.180 Angle : 0.496 5.729 10398 Z= 0.256 Chirality : 0.044 0.143 1185 Planarity : 0.004 0.054 1350 Dihedral : 9.285 89.557 1293 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.61 % Allowed : 16.60 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.65 (0.27), residues: 942 helix: 1.31 (0.42), residues: 180 sheet: 0.83 (0.27), residues: 318 loop : -0.17 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 262 HIS 0.001 0.000 HIS C 132 PHE 0.010 0.001 PHE A 297 TYR 0.014 0.001 TYR C 318 ARG 0.003 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.809 Fit side-chains REVERT: A 172 LYS cc_start: 0.8225 (tppt) cc_final: 0.7812 (mttp) REVERT: A 259 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8399 (pt0) REVERT: A 285 LYS cc_start: 0.8420 (mttt) cc_final: 0.7967 (mttp) REVERT: B 320 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8934 (mm) REVERT: B 346 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7201 (mp) REVERT: C 265 ASP cc_start: 0.8516 (t0) cc_final: 0.8034 (t0) REVERT: C 267 ASP cc_start: 0.7231 (m-30) cc_final: 0.6636 (m-30) REVERT: C 320 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8754 (mm) outliers start: 20 outliers final: 6 residues processed: 90 average time/residue: 0.2029 time to fit residues: 25.0486 Evaluate side-chains 82 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 57 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 0.0020 chunk 75 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 0.0000 overall best weight: 0.1970 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7623 Z= 0.129 Angle : 0.474 8.247 10398 Z= 0.241 Chirality : 0.042 0.132 1185 Planarity : 0.003 0.044 1350 Dihedral : 8.244 86.656 1293 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.35 % Allowed : 17.78 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.80 (0.27), residues: 942 helix: 1.68 (0.44), residues: 162 sheet: 0.94 (0.27), residues: 318 loop : -0.11 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 167 HIS 0.000 0.000 HIS A 132 PHE 0.009 0.001 PHE A 102 TYR 0.011 0.001 TYR A 318 ARG 0.002 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.858 Fit side-chains REVERT: A 172 LYS cc_start: 0.8204 (tppt) cc_final: 0.7846 (mttp) REVERT: B 118 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7016 (mmtm) REVERT: C 108 MET cc_start: 0.8847 (ppp) cc_final: 0.8393 (ptt) REVERT: C 265 ASP cc_start: 0.8535 (t0) cc_final: 0.8064 (t0) REVERT: C 267 ASP cc_start: 0.7228 (m-30) cc_final: 0.6617 (m-30) REVERT: C 346 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7414 (mp) outliers start: 18 outliers final: 4 residues processed: 87 average time/residue: 0.2060 time to fit residues: 24.5269 Evaluate side-chains 73 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 346 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7623 Z= 0.235 Angle : 0.515 7.964 10398 Z= 0.264 Chirality : 0.044 0.143 1185 Planarity : 0.004 0.040 1350 Dihedral : 7.588 85.304 1293 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.35 % Allowed : 19.22 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.46 (0.27), residues: 942 helix: 0.84 (0.41), residues: 198 sheet: 0.92 (0.27), residues: 318 loop : -0.37 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 262 HIS 0.001 0.001 HIS B 132 PHE 0.011 0.001 PHE A 297 TYR 0.015 0.001 TYR A 318 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.757 Fit side-chains REVERT: A 172 LYS cc_start: 0.8256 (tppt) cc_final: 0.7890 (mttp) REVERT: B 320 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8941 (mm) REVERT: B 346 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7266 (mp) REVERT: C 108 MET cc_start: 0.8954 (ppp) cc_final: 0.8431 (ptt) REVERT: C 320 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8749 (mm) REVERT: C 346 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7275 (mp) outliers start: 18 outliers final: 9 residues processed: 93 average time/residue: 0.2129 time to fit residues: 26.5629 Evaluate side-chains 86 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 346 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7623 Z= 0.232 Angle : 0.524 7.720 10398 Z= 0.269 Chirality : 0.044 0.143 1185 Planarity : 0.004 0.036 1350 Dihedral : 7.133 84.615 1293 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.27 % Allowed : 19.22 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.34 (0.27), residues: 942 helix: 0.83 (0.41), residues: 198 sheet: 0.79 (0.27), residues: 324 loop : -0.45 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 167 HIS 0.001 0.001 HIS B 132 PHE 0.010 0.001 PHE A 297 TYR 0.015 0.001 TYR A 318 ARG 0.003 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 0.868 Fit side-chains REVERT: A 172 LYS cc_start: 0.8266 (tppt) cc_final: 0.7932 (mttp) REVERT: B 320 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8882 (mm) REVERT: B 346 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7373 (mp) REVERT: C 108 MET cc_start: 0.8986 (ppp) cc_final: 0.8464 (ptt) REVERT: C 320 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8736 (mm) outliers start: 25 outliers final: 9 residues processed: 99 average time/residue: 0.2124 time to fit residues: 28.4500 Evaluate side-chains 87 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7623 Z= 0.295 Angle : 0.568 8.670 10398 Z= 0.292 Chirality : 0.045 0.152 1185 Planarity : 0.004 0.033 1350 Dihedral : 7.171 84.710 1293 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.27 % Allowed : 19.61 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.24 (0.27), residues: 942 helix: 0.80 (0.41), residues: 198 sheet: 0.73 (0.27), residues: 324 loop : -0.55 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 262 HIS 0.002 0.001 HIS B 132 PHE 0.011 0.002 PHE A 299 TYR 0.016 0.001 TYR A 318 ARG 0.003 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.832 Fit side-chains REVERT: A 172 LYS cc_start: 0.8296 (tppt) cc_final: 0.7973 (mttp) REVERT: A 256 MET cc_start: 0.8569 (mmm) cc_final: 0.8269 (tpp) REVERT: A 259 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8354 (pt0) REVERT: B 267 ASP cc_start: 0.7617 (m-30) cc_final: 0.7228 (m-30) REVERT: B 320 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8905 (mm) REVERT: C 108 MET cc_start: 0.9006 (ppp) cc_final: 0.8481 (ptt) REVERT: C 172 LYS cc_start: 0.8217 (tppt) cc_final: 0.7581 (mttt) REVERT: C 320 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8740 (mm) outliers start: 25 outliers final: 16 residues processed: 105 average time/residue: 0.1947 time to fit residues: 27.8954 Evaluate side-chains 96 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.0470 chunk 89 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7623 Z= 0.212 Angle : 0.537 8.749 10398 Z= 0.275 Chirality : 0.044 0.143 1185 Planarity : 0.003 0.032 1350 Dihedral : 7.187 84.650 1293 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.79 % Allowed : 19.48 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.34 (0.27), residues: 942 helix: 0.86 (0.41), residues: 198 sheet: 0.87 (0.27), residues: 318 loop : -0.53 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 262 HIS 0.001 0.001 HIS A 132 PHE 0.010 0.001 PHE A 299 TYR 0.014 0.001 TYR A 318 ARG 0.002 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 0.850 Fit side-chains REVERT: A 118 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7271 (mmtp) REVERT: A 172 LYS cc_start: 0.8326 (tppt) cc_final: 0.8008 (mttp) REVERT: A 256 MET cc_start: 0.8561 (mmm) cc_final: 0.8282 (tpp) REVERT: A 259 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8328 (pt0) REVERT: B 267 ASP cc_start: 0.7593 (m-30) cc_final: 0.7205 (m-30) REVERT: B 320 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8885 (mm) REVERT: C 108 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8446 (ptt) REVERT: C 172 LYS cc_start: 0.8177 (tppt) cc_final: 0.7539 (mttt) REVERT: C 320 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8737 (mm) outliers start: 29 outliers final: 18 residues processed: 96 average time/residue: 0.2057 time to fit residues: 26.6680 Evaluate side-chains 93 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 70 optimal weight: 0.0670 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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: 0.7916 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7623 Z= 0.139 Angle : 0.488 7.266 10398 Z= 0.248 Chirality : 0.042 0.131 1185 Planarity : 0.003 0.030 1350 Dihedral : 6.647 82.059 1293 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.35 % Allowed : 20.78 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.55 (0.27), residues: 942 helix: 1.19 (0.43), residues: 180 sheet: 1.06 (0.28), residues: 315 loop : -0.47 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 167 HIS 0.001 0.000 HIS C 132 PHE 0.008 0.001 PHE A 297 TYR 0.011 0.001 TYR C 318 ARG 0.003 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.843 Fit side-chains REVERT: A 118 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7259 (mmtp) REVERT: A 172 LYS cc_start: 0.8301 (tppt) cc_final: 0.7970 (mttp) REVERT: C 108 MET cc_start: 0.8948 (ppp) cc_final: 0.8390 (ptt) REVERT: C 172 LYS cc_start: 0.8198 (tppt) cc_final: 0.7617 (mttt) outliers start: 18 outliers final: 9 residues processed: 89 average time/residue: 0.2199 time to fit residues: 26.2641 Evaluate side-chains 75 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain C residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 0.0270 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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: 0.7944 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7623 Z= 0.176 Angle : 0.505 7.184 10398 Z= 0.257 Chirality : 0.043 0.136 1185 Planarity : 0.003 0.030 1350 Dihedral : 6.537 80.638 1293 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.83 % Allowed : 21.44 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.55 (0.27), residues: 942 helix: 0.93 (0.41), residues: 198 sheet: 1.07 (0.27), residues: 318 loop : -0.41 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.001 0.000 HIS C 132 PHE 0.009 0.001 PHE A 297 TYR 0.013 0.001 TYR C 318 ARG 0.002 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.949 Fit side-chains REVERT: A 118 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7303 (mmtp) REVERT: A 172 LYS cc_start: 0.8338 (tppt) cc_final: 0.8009 (mttp) REVERT: C 108 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8397 (ptt) REVERT: C 172 LYS cc_start: 0.8192 (tppt) cc_final: 0.7603 (mttt) outliers start: 14 outliers final: 12 residues processed: 78 average time/residue: 0.2364 time to fit residues: 24.5402 Evaluate side-chains 80 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 7623 Z= 0.481 Angle : 0.661 8.846 10398 Z= 0.343 Chirality : 0.048 0.172 1185 Planarity : 0.005 0.034 1350 Dihedral : 7.430 83.901 1293 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.09 % Allowed : 21.31 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.15 (0.26), residues: 942 helix: 0.22 (0.41), residues: 198 sheet: 0.77 (0.27), residues: 303 loop : -0.84 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 87 HIS 0.001 0.001 HIS C 132 PHE 0.014 0.002 PHE C 299 TYR 0.020 0.002 TYR A 318 ARG 0.004 0.001 ARG A 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.878 Fit side-chains REVERT: A 118 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7281 (mmtp) REVERT: A 172 LYS cc_start: 0.8374 (tppt) cc_final: 0.8078 (mttp) REVERT: A 256 MET cc_start: 0.8635 (mmm) cc_final: 0.8400 (tpp) REVERT: B 320 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8824 (mm) REVERT: C 58 GLN cc_start: 0.7631 (tp40) cc_final: 0.7390 (mm-40) REVERT: C 108 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8537 (ptt) REVERT: C 172 LYS cc_start: 0.8295 (tppt) cc_final: 0.7699 (mttt) REVERT: C 214 SER cc_start: 0.8054 (p) cc_final: 0.7831 (t) outliers start: 16 outliers final: 14 residues processed: 96 average time/residue: 0.2347 time to fit residues: 30.0790 Evaluate side-chains 90 residues out of total 831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 chunk 13 optimal weight: 0.0070 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.172475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110865 restraints weight = 7521.537| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.99 r_work: 0.3026 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7623 Z= 0.190 Angle : 0.530 7.768 10398 Z= 0.271 Chirality : 0.044 0.152 1185 Planarity : 0.004 0.031 1350 Dihedral : 7.048 84.559 1293 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.75 % Allowed : 21.96 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.30 (0.27), residues: 942 helix: 0.90 (0.44), residues: 180 sheet: 0.87 (0.27), residues: 318 loop : -0.55 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 167 HIS 0.001 0.001 HIS C 132 PHE 0.010 0.001 PHE B 297 TYR 0.014 0.001 TYR A 318 ARG 0.003 0.000 ARG C 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.36 seconds wall clock time: 33 minutes 43.28 seconds (2023.28 seconds total)