Starting phenix.real_space_refine on Fri Aug 2 22:46:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/08_2024/8ur7_42486.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/08_2024/8ur7_42486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/08_2024/8ur7_42486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/08_2024/8ur7_42486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/08_2024/8ur7_42486.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/08_2024/8ur7_42486.cif" } resolution = 3.9 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= 0.003 sd= 0.115 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 18 5.16 5 C 3795 2.51 5 N 999 2.21 5 O 960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5772 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1882 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 21, 'ASN:plan1': 9, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 154 Chain: "B" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1882 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 21, 'ASN:plan1': 9, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 154 Chain: "C" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1882 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 21, 'ASN:plan1': 9, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 154 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.90, per 1000 atoms: 0.68 Number of scatterers: 5772 At special positions: 0 Unit cell: (82.8298, 85.686, 119.96, 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 18 16.00 O 960 8.00 N 999 7.00 C 3795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.10 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 271 " distance=2.18 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.10 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 139 " distance=2.02 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 271 " distance=2.18 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.10 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 271 " distance=2.18 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 501 " - " ASN A 58 " " NAG A 502 " - " ASN A 163 " " NAG A 503 " - " ASN A 129 " " NAG B 501 " - " ASN B 58 " " NAG B 502 " - " ASN B 163 " " NAG B 503 " - " ASN B 129 " " NAG C 501 " - " ASN C 58 " " NAG C 502 " - " ASN C 163 " " NAG C 503 " - " ASN C 129 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 27.0% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 270 through 313 Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 270 through 313 Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 270 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.478A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 119 removed outlier: 6.478A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.469A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.478A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 115 through 119 removed outlier: 6.478A pdb=" N TYR B 256 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.470A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER B 146 " --> pdb=" O CYS B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AA9, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.479A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.479A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.470A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 169 309 hydrogen bonds defined for protein. 864 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: 1.66 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1182 1.33 - 1.45: 1482 1.45 - 1.57: 3267 1.57 - 1.69: 3 1.69 - 1.81: 18 Bond restraints: 5952 Sorted by residual: bond pdb=" C ALA C 52 " pdb=" N PRO C 53 " ideal model delta sigma weight residual 1.335 1.361 -0.026 9.40e-03 1.13e+04 7.48e+00 bond pdb=" C5 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C5 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C ALA A 52 " pdb=" N PRO A 53 " ideal model delta sigma weight residual 1.335 1.360 -0.025 9.40e-03 1.13e+04 7.28e+00 bond pdb=" C5 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.28e+00 ... (remaining 5947 not shown) Histogram of bond angle deviations from ideal: 101.56 - 108.11: 324 108.11 - 114.66: 3319 114.66 - 121.21: 2943 121.21 - 127.76: 1524 127.76 - 134.31: 77 Bond angle restraints: 8187 Sorted by residual: angle pdb=" C HIS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta sigma weight residual 119.66 126.50 -6.84 7.30e-01 1.88e+00 8.79e+01 angle pdb=" C HIS B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta sigma weight residual 119.66 126.48 -6.82 7.30e-01 1.88e+00 8.73e+01 angle pdb=" C HIS C 184 " pdb=" N PRO C 185 " pdb=" CA PRO C 185 " ideal model delta sigma weight residual 119.66 126.44 -6.78 7.30e-01 1.88e+00 8.63e+01 angle pdb=" C ASN B 88 " pdb=" N PRO B 89 " pdb=" CA PRO B 89 " ideal model delta sigma weight residual 120.31 127.70 -7.39 9.80e-01 1.04e+00 5.69e+01 angle pdb=" C ASN A 88 " pdb=" N PRO A 89 " pdb=" CA PRO A 89 " ideal model delta sigma weight residual 120.31 127.67 -7.36 9.80e-01 1.04e+00 5.63e+01 ... (remaining 8182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3396 17.27 - 34.53: 87 34.53 - 51.80: 18 51.80 - 69.07: 0 69.07 - 86.33: 9 Dihedral angle restraints: 3510 sinusoidal: 1212 harmonic: 2298 Sorted by residual: dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sinusoidal sigma weight residual 93.00 173.12 -80.12 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS B 94 " pdb=" SG CYS B 94 " pdb=" SG CYS B 139 " pdb=" CB CYS B 139 " ideal model delta sinusoidal sigma weight residual 93.00 173.11 -80.11 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 173.10 -80.10 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 3507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 659 0.065 - 0.130: 210 0.130 - 0.194: 52 0.194 - 0.259: 18 0.259 - 0.324: 9 Chirality restraints: 948 Sorted by residual: chirality pdb=" C2 NAG C 502 " pdb=" C1 NAG C 502 " pdb=" C3 NAG C 502 " pdb=" N2 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C2 NAG B 502 " pdb=" C1 NAG B 502 " pdb=" C3 NAG B 502 " pdb=" N2 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C2 NAG A 502 " pdb=" C1 NAG A 502 " pdb=" C3 NAG A 502 " pdb=" N2 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 945 not shown) Planarity restraints: 1041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 232 " 0.025 2.00e-02 2.50e+03 1.36e-02 3.72e+00 pdb=" CG TYR C 232 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR C 232 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 232 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR C 232 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 232 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 232 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 232 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 232 " 0.025 2.00e-02 2.50e+03 1.36e-02 3.71e+00 pdb=" CG TYR B 232 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR B 232 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 232 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 232 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 232 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 232 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 232 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 232 " 0.025 2.00e-02 2.50e+03 1.36e-02 3.68e+00 pdb=" CG TYR A 232 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 232 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 232 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 232 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 232 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 232 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 232 " 0.020 2.00e-02 2.50e+03 ... (remaining 1038 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 529 2.75 - 3.28: 5585 3.28 - 3.82: 9305 3.82 - 4.36: 10789 4.36 - 4.90: 17958 Nonbonded interactions: 44166 Sorted by model distance: nonbonded pdb=" CB PRO A 53 " pdb=" CE1 TYR A 82 " model vdw 2.207 3.740 nonbonded pdb=" CB PRO B 53 " pdb=" CE1 TYR B 82 " model vdw 2.207 3.740 nonbonded pdb=" CB PRO C 53 " pdb=" CE1 TYR C 82 " model vdw 2.207 3.740 nonbonded pdb=" O GLU A 309 " pdb=" N ASN A 312 " model vdw 2.399 3.120 nonbonded pdb=" O GLU C 309 " pdb=" N ASN C 312 " model vdw 2.399 3.120 ... (remaining 44161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.640 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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 : 0.009 0.054 5952 Z= 0.630 Angle : 1.277 8.129 8187 Z= 0.892 Chirality : 0.075 0.324 948 Planarity : 0.005 0.018 1032 Dihedral : 9.351 86.333 2013 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.66 % Allowed : 3.31 % Favored : 96.03 % 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: -0.32 (0.27), residues: 783 helix: 0.32 (0.34), residues: 201 sheet: 1.20 (0.31), residues: 198 loop : -1.30 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 80 HIS 0.003 0.001 HIS A 130 PHE 0.013 0.003 PHE B 115 TYR 0.025 0.005 TYR B 232 ARG 0.002 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TYR cc_start: 0.9012 (t80) cc_final: 0.8386 (t80) REVERT: B 172 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8595 (mmtt) REVERT: B 223 VAL cc_start: 0.9057 (t) cc_final: 0.8570 (p) REVERT: B 229 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.8225 (mmt90) REVERT: B 295 HIS cc_start: 0.8473 (t70) cc_final: 0.7975 (t-170) REVERT: C 102 TYR cc_start: 0.9060 (t80) cc_final: 0.8738 (t80) REVERT: C 147 PHE cc_start: 0.6582 (t80) cc_final: 0.6143 (t80) REVERT: C 172 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8519 (mmmt) outliers start: 3 outliers final: 0 residues processed: 161 average time/residue: 0.2231 time to fit residues: 44.1384 Evaluate side-chains 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 108 GLN C 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5952 Z= 0.246 Angle : 0.625 6.932 8187 Z= 0.337 Chirality : 0.046 0.199 948 Planarity : 0.004 0.026 1032 Dihedral : 7.263 97.382 1038 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.65 % Allowed : 13.69 % Favored : 83.66 % 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: 0.33 (0.28), residues: 783 helix: 1.53 (0.36), residues: 210 sheet: 1.21 (0.33), residues: 204 loop : -1.19 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 153 HIS 0.004 0.001 HIS C 183 PHE 0.027 0.002 PHE A 115 TYR 0.014 0.002 TYR C 195 ARG 0.004 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 HIS cc_start: 0.8447 (t70) cc_final: 0.8167 (t-170) REVERT: B 300 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8919 (tt) REVERT: C 172 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8591 (mmtt) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.1955 time to fit residues: 28.6932 Evaluate side-chains 101 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 302 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 191 GLN A 250 ASN B 191 GLN B 250 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 250 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5952 Z= 0.208 Angle : 0.558 8.311 8187 Z= 0.301 Chirality : 0.044 0.212 948 Planarity : 0.004 0.027 1032 Dihedral : 7.019 98.949 1038 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.19 % Allowed : 13.47 % Favored : 82.34 % 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: 0.38 (0.29), residues: 783 helix: 1.85 (0.36), residues: 210 sheet: 1.05 (0.34), residues: 195 loop : -1.17 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 153 HIS 0.007 0.001 HIS C 295 PHE 0.028 0.002 PHE A 115 TYR 0.018 0.002 TYR A 301 ARG 0.005 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8255 (tmm-80) REVERT: B 82 TYR cc_start: 0.7035 (p90) cc_final: 0.6575 (p90) REVERT: C 168 TYR cc_start: 0.7376 (t80) cc_final: 0.7040 (t80) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 0.1722 time to fit residues: 23.7451 Evaluate side-chains 87 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5952 Z= 0.312 Angle : 0.612 10.193 8187 Z= 0.329 Chirality : 0.046 0.274 948 Planarity : 0.004 0.041 1032 Dihedral : 6.968 95.788 1038 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.42 % Allowed : 14.13 % Favored : 81.46 % 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: 0.23 (0.29), residues: 783 helix: 1.67 (0.37), residues: 204 sheet: 0.84 (0.35), residues: 195 loop : -1.09 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 127 HIS 0.009 0.001 HIS B 295 PHE 0.026 0.002 PHE A 115 TYR 0.016 0.002 TYR A 195 ARG 0.005 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9370 (t80) cc_final: 0.8866 (t80) REVERT: A 106 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.7972 (tmm-80) REVERT: B 82 TYR cc_start: 0.7062 (p90) cc_final: 0.6580 (p90) REVERT: B 102 TYR cc_start: 0.9176 (t80) cc_final: 0.8906 (t80) REVERT: C 106 ARG cc_start: 0.8532 (ttp-110) cc_final: 0.8061 (ttp-170) outliers start: 20 outliers final: 13 residues processed: 103 average time/residue: 0.1762 time to fit residues: 23.6133 Evaluate side-chains 93 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 302 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN C 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5952 Z= 0.198 Angle : 0.563 8.476 8187 Z= 0.295 Chirality : 0.044 0.196 948 Planarity : 0.004 0.025 1032 Dihedral : 6.695 93.103 1038 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.65 % Allowed : 16.78 % Favored : 80.57 % 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: 0.43 (0.30), residues: 783 helix: 2.00 (0.39), residues: 207 sheet: 0.82 (0.37), residues: 195 loop : -1.01 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.009 0.001 HIS B 295 PHE 0.026 0.002 PHE A 115 TYR 0.023 0.002 TYR A 195 ARG 0.005 0.001 ARG C 305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8210 (tmm-80) REVERT: B 82 TYR cc_start: 0.7042 (p90) cc_final: 0.6664 (p90) REVERT: B 102 TYR cc_start: 0.9241 (t80) cc_final: 0.8933 (t80) REVERT: C 106 ARG cc_start: 0.8530 (ttp-110) cc_final: 0.8050 (ttp-170) REVERT: C 305 ARG cc_start: 0.7815 (mmt90) cc_final: 0.7570 (tpp-160) outliers start: 12 outliers final: 11 residues processed: 97 average time/residue: 0.2258 time to fit residues: 27.3878 Evaluate side-chains 90 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 HIS C 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5952 Z= 0.186 Angle : 0.558 10.403 8187 Z= 0.294 Chirality : 0.045 0.275 948 Planarity : 0.003 0.025 1032 Dihedral : 6.636 90.900 1038 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.43 % Allowed : 17.22 % Favored : 80.35 % 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: 0.44 (0.30), residues: 783 helix: 2.07 (0.39), residues: 207 sheet: 0.77 (0.37), residues: 195 loop : -1.01 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 180 HIS 0.006 0.001 HIS B 295 PHE 0.027 0.002 PHE A 115 TYR 0.022 0.001 TYR A 195 ARG 0.004 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8773 (ttp-110) cc_final: 0.8158 (tmm-80) REVERT: B 82 TYR cc_start: 0.7118 (p90) cc_final: 0.6762 (p90) REVERT: B 102 TYR cc_start: 0.9233 (t80) cc_final: 0.8884 (t80) REVERT: C 66 LEU cc_start: 0.8749 (mp) cc_final: 0.8521 (mp) REVERT: C 106 ARG cc_start: 0.8568 (ttp-110) cc_final: 0.8116 (ttp-170) REVERT: C 305 ARG cc_start: 0.7831 (mmt90) cc_final: 0.7527 (tpp-160) outliers start: 11 outliers final: 10 residues processed: 96 average time/residue: 0.2081 time to fit residues: 25.4127 Evaluate side-chains 88 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0060 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5952 Z= 0.187 Angle : 0.551 8.486 8187 Z= 0.289 Chirality : 0.044 0.197 948 Planarity : 0.004 0.025 1032 Dihedral : 6.506 88.241 1038 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.99 % Allowed : 17.44 % Favored : 80.57 % 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: 0.37 (0.30), residues: 783 helix: 2.05 (0.39), residues: 207 sheet: 0.81 (0.39), residues: 189 loop : -1.10 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 180 HIS 0.004 0.001 HIS C 295 PHE 0.029 0.002 PHE A 115 TYR 0.025 0.002 TYR B 168 ARG 0.004 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8773 (ttp-110) cc_final: 0.8170 (tmm-80) REVERT: B 82 TYR cc_start: 0.7080 (p90) cc_final: 0.6738 (p90) REVERT: B 102 TYR cc_start: 0.9253 (t80) cc_final: 0.8832 (t80) outliers start: 9 outliers final: 8 residues processed: 92 average time/residue: 0.1961 time to fit residues: 23.3321 Evaluate side-chains 84 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.7389 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5952 Z= 0.229 Angle : 0.566 8.512 8187 Z= 0.298 Chirality : 0.044 0.180 948 Planarity : 0.004 0.026 1032 Dihedral : 6.374 83.663 1038 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 2.21 % Allowed : 17.66 % Favored : 80.13 % 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: 0.30 (0.30), residues: 783 helix: 1.92 (0.39), residues: 207 sheet: 0.78 (0.39), residues: 189 loop : -1.11 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.004 0.001 HIS C 295 PHE 0.028 0.002 PHE A 115 TYR 0.024 0.002 TYR C 195 ARG 0.005 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9249 (t80) cc_final: 0.8701 (t80) REVERT: A 106 ARG cc_start: 0.8782 (ttp-110) cc_final: 0.8046 (tmm-80) REVERT: B 82 TYR cc_start: 0.7075 (p90) cc_final: 0.6782 (p90) REVERT: B 102 TYR cc_start: 0.9299 (t80) cc_final: 0.8882 (t80) REVERT: C 106 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8112 (ttp-170) outliers start: 10 outliers final: 10 residues processed: 93 average time/residue: 0.1923 time to fit residues: 23.1228 Evaluate side-chains 83 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5952 Z= 0.236 Angle : 0.568 8.449 8187 Z= 0.302 Chirality : 0.044 0.201 948 Planarity : 0.004 0.026 1032 Dihedral : 6.254 80.215 1038 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.30 % Favored : 97.32 % Rotamer: Outliers : 2.43 % Allowed : 19.21 % Favored : 78.37 % 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: 0.21 (0.30), residues: 783 helix: 1.81 (0.39), residues: 207 sheet: 0.74 (0.39), residues: 189 loop : -1.14 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.004 0.001 HIS C 295 PHE 0.029 0.002 PHE A 115 TYR 0.027 0.002 TYR C 195 ARG 0.003 0.001 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9251 (t80) cc_final: 0.8722 (t80) REVERT: A 106 ARG cc_start: 0.8770 (ttp-110) cc_final: 0.8068 (tmm-80) REVERT: A 304 GLU cc_start: 0.8041 (tt0) cc_final: 0.7698 (tp30) REVERT: B 82 TYR cc_start: 0.7118 (p90) cc_final: 0.6805 (p90) REVERT: B 102 TYR cc_start: 0.9284 (t80) cc_final: 0.8907 (t80) REVERT: B 106 ARG cc_start: 0.8754 (tmm-80) cc_final: 0.8300 (ttp-110) REVERT: B 255 TRP cc_start: 0.8314 (t60) cc_final: 0.8043 (t60) REVERT: C 106 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8214 (ttp-170) REVERT: C 304 GLU cc_start: 0.8194 (tp30) cc_final: 0.7473 (tp30) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 0.1786 time to fit residues: 21.9828 Evaluate side-chains 84 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 5952 Z= 0.418 Angle : 0.655 8.166 8187 Z= 0.357 Chirality : 0.046 0.185 948 Planarity : 0.005 0.038 1032 Dihedral : 6.418 77.488 1038 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.19 % Favored : 96.42 % Rotamer: Outliers : 2.43 % Allowed : 18.98 % Favored : 78.59 % 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: -0.30 (0.30), residues: 783 helix: 1.28 (0.38), residues: 201 sheet: 0.33 (0.38), residues: 195 loop : -1.30 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 80 HIS 0.006 0.001 HIS A 183 PHE 0.033 0.003 PHE C 115 TYR 0.026 0.002 TYR C 195 ARG 0.006 0.001 ARG B 305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8755 (ttp-110) cc_final: 0.8154 (tmm-80) REVERT: A 280 TYR cc_start: 0.7512 (t80) cc_final: 0.7214 (t80) REVERT: A 304 GLU cc_start: 0.8220 (tt0) cc_final: 0.7775 (tp30) REVERT: B 82 TYR cc_start: 0.7069 (p90) cc_final: 0.6717 (p90) REVERT: B 255 TRP cc_start: 0.8399 (t60) cc_final: 0.8088 (t60) REVERT: C 278 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7981 (mtpt) outliers start: 11 outliers final: 10 residues processed: 76 average time/residue: 0.2055 time to fit residues: 20.0116 Evaluate side-chains 68 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 170 ASN Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.177660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143269 restraints weight = 8203.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144860 restraints weight = 6756.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145708 restraints weight = 5940.699| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5952 Z= 0.212 Angle : 0.576 8.339 8187 Z= 0.304 Chirality : 0.044 0.180 948 Planarity : 0.004 0.028 1032 Dihedral : 6.237 75.582 1038 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.04 % Favored : 97.57 % Rotamer: Outliers : 2.43 % Allowed : 19.65 % Favored : 77.92 % 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: -0.15 (0.30), residues: 783 helix: 1.65 (0.39), residues: 201 sheet: 0.47 (0.43), residues: 153 loop : -1.22 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 234 HIS 0.004 0.001 HIS C 295 PHE 0.031 0.002 PHE C 115 TYR 0.024 0.001 TYR C 195 ARG 0.003 0.001 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1355.72 seconds wall clock time: 24 minutes 39.95 seconds (1479.95 seconds total)