Starting phenix.real_space_refine on Tue Feb 13 11:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/02_2024/8ur7_42486.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/02_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_42486/02_2024/8ur7_42486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/02_2024/8ur7_42486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/02_2024/8ur7_42486.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur7_42486/02_2024/8ur7_42486.pdb" } 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-5238/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: 3.77, per 1000 atoms: 0.65 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: 2.16 Conformation dependent library (CDL) restraints added in 1.2 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: 0.73 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: 1.74 Time building geometry restraints manager: 2.37 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 2.520 nonbonded pdb=" O GLU C 309 " pdb=" N ASN C 312 " model vdw 2.399 2.520 ... (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 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: 0.280 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: 1.570 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.280 Find NCS groups from input model: 0.370 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- 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 : 0.655 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: 0.2259 time to fit residues: 44.6614 Evaluate side-chains 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 0.4980 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 170 ASN B 108 GLN C 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5952 Z= 0.232 Angle : 0.608 6.281 8187 Z= 0.329 Chirality : 0.046 0.222 948 Planarity : 0.004 0.027 1032 Dihedral : 7.393 99.446 1038 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.31 % Allowed : 12.80 % Favored : 83.89 % 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 (0.28), residues: 783 helix: 1.64 (0.36), residues: 210 sheet: 1.19 (0.32), residues: 204 loop : -1.18 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 153 HIS 0.003 0.001 HIS A 183 PHE 0.028 0.002 PHE A 115 TYR 0.014 0.002 TYR A 168 ARG 0.004 0.001 ARG C 305 *********************** 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 122 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 HIS cc_start: 0.8469 (t70) cc_final: 0.8194 (t-170) REVERT: C 102 TYR cc_start: 0.9147 (t80) cc_final: 0.8925 (t80) REVERT: C 106 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.7945 (ttp-170) outliers start: 15 outliers final: 12 residues processed: 118 average time/residue: 0.2058 time to fit residues: 30.6412 Evaluate side-chains 101 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 302 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 THR 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: 0.8980 chunk 21 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5952 Z= 0.186 Angle : 0.539 8.277 8187 Z= 0.291 Chirality : 0.044 0.215 948 Planarity : 0.004 0.025 1032 Dihedral : 6.897 97.516 1038 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.31 % Allowed : 15.01 % Favored : 81.68 % 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: 0.46 (0.29), residues: 783 helix: 2.06 (0.37), residues: 210 sheet: 1.06 (0.34), residues: 195 loop : -1.20 (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 0.026 0.002 PHE A 115 TYR 0.015 0.002 TYR A 195 ARG 0.005 0.001 ARG B 117 *********************** 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: 15 poor density : 95 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8297 (tmm-80) REVERT: B 82 TYR cc_start: 0.6990 (p90) cc_final: 0.6516 (p90) REVERT: C 102 TYR cc_start: 0.9169 (t80) cc_final: 0.8817 (t80) REVERT: C 106 ARG cc_start: 0.8698 (ttp-110) cc_final: 0.7984 (ttp-170) REVERT: C 168 TYR cc_start: 0.7555 (t80) cc_final: 0.7263 (t80) outliers start: 15 outliers final: 12 residues processed: 109 average time/residue: 0.2055 time to fit residues: 28.1604 Evaluate side-chains 90 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 150 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 170 ASN 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: 3.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 5952 Z= 0.354 Angle : 0.609 8.376 8187 Z= 0.328 Chirality : 0.045 0.253 948 Planarity : 0.004 0.029 1032 Dihedral : 6.861 94.386 1038 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.97 % Allowed : 16.11 % Favored : 79.91 % 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: 0.20 (0.29), residues: 783 helix: 1.60 (0.37), residues: 210 sheet: 0.86 (0.35), residues: 195 loop : -1.15 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 127 HIS 0.008 0.001 HIS B 295 PHE 0.026 0.003 PHE A 115 TYR 0.017 0.002 TYR A 195 ARG 0.006 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 104 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9424 (t80) cc_final: 0.9158 (t80) REVERT: B 82 TYR cc_start: 0.7062 (p90) cc_final: 0.6604 (p90) REVERT: B 102 TYR cc_start: 0.9218 (t80) cc_final: 0.8902 (t80) REVERT: C 106 ARG cc_start: 0.8471 (ttp-110) cc_final: 0.7918 (ttp-170) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.1926 time to fit residues: 25.6016 Evaluate side-chains 96 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 271 CYS 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 150 ASN Chi-restraints excluded: chain C residue 155 THR 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: 0.9980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7380 moved from start: 0.3884 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= 0.200 Angle : 0.551 8.634 8187 Z= 0.287 Chirality : 0.044 0.201 948 Planarity : 0.003 0.023 1032 Dihedral : 6.586 91.776 1038 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.31 % Allowed : 18.32 % 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: 0.42 (0.30), residues: 783 helix: 1.88 (0.38), residues: 213 sheet: 0.87 (0.37), residues: 195 loop : -1.04 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.007 0.001 HIS B 295 PHE 0.025 0.002 PHE A 115 TYR 0.020 0.001 TYR A 195 ARG 0.004 0.001 ARG A 117 *********************** 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 96 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TYR cc_start: 0.7153 (p90) cc_final: 0.6764 (p90) REVERT: B 102 TYR cc_start: 0.9226 (t80) cc_final: 0.8895 (t80) REVERT: C 106 ARG cc_start: 0.8521 (ttp-110) cc_final: 0.8040 (ttp-170) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.2042 time to fit residues: 24.3740 Evaluate side-chains 90 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 150 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 THR 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: 0.5980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** 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: 0.7366 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5952 Z= 0.203 Angle : 0.578 10.296 8187 Z= 0.302 Chirality : 0.045 0.289 948 Planarity : 0.003 0.023 1032 Dihedral : 6.613 89.788 1038 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.87 % Allowed : 18.54 % 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: 0.43 (0.31), residues: 783 helix: 1.95 (0.39), residues: 207 sheet: 0.81 (0.37), residues: 195 loop : -0.97 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.006 0.001 HIS B 295 PHE 0.027 0.002 PHE A 115 TYR 0.023 0.001 TYR A 195 ARG 0.004 0.001 ARG A 106 *********************** 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 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 TYR cc_start: 0.7120 (p90) cc_final: 0.6745 (p90) REVERT: B 102 TYR cc_start: 0.9232 (t80) cc_final: 0.8796 (t80) REVERT: C 106 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.8114 (ttp-170) outliers start: 13 outliers final: 12 residues processed: 94 average time/residue: 0.2090 time to fit residues: 24.9892 Evaluate side-chains 87 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 THR 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: 8.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5952 Z= 0.266 Angle : 0.582 8.362 8187 Z= 0.311 Chirality : 0.045 0.184 948 Planarity : 0.004 0.024 1032 Dihedral : 6.565 87.003 1038 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.09 % Allowed : 17.44 % Favored : 79.47 % 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: 0.25 (0.30), residues: 783 helix: 1.80 (0.39), residues: 207 sheet: 0.77 (0.38), residues: 189 loop : -1.10 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 180 HIS 0.005 0.001 HIS B 295 PHE 0.028 0.002 PHE A 115 TYR 0.041 0.002 TYR B 168 ARG 0.003 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 100 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9350 (t80) cc_final: 0.8923 (t80) REVERT: A 106 ARG cc_start: 0.8920 (ttp-110) cc_final: 0.7995 (tmm-80) REVERT: B 82 TYR cc_start: 0.7154 (p90) cc_final: 0.6849 (p90) REVERT: B 102 TYR cc_start: 0.9255 (t80) cc_final: 0.8836 (t80) REVERT: C 305 ARG cc_start: 0.7773 (mmt90) cc_final: 0.7564 (tpt170) outliers start: 14 outliers final: 12 residues processed: 98 average time/residue: 0.1925 time to fit residues: 24.2424 Evaluate side-chains 84 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 150 ASN Chi-restraints excluded: chain C residue 155 THR 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: 8.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 70 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5952 Z= 0.172 Angle : 0.552 8.562 8187 Z= 0.288 Chirality : 0.044 0.195 948 Planarity : 0.003 0.025 1032 Dihedral : 6.402 84.365 1038 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.65 % Allowed : 19.21 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 783 helix: 2.08 (0.39), residues: 207 sheet: 0.80 (0.39), residues: 189 loop : -1.08 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 180 HIS 0.005 0.001 HIS B 295 PHE 0.028 0.002 PHE A 115 TYR 0.025 0.001 TYR A 195 ARG 0.003 0.000 ARG A 117 *********************** 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 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9299 (t80) cc_final: 0.8822 (t80) REVERT: A 106 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.7977 (tmm-80) REVERT: B 82 TYR cc_start: 0.7079 (p90) cc_final: 0.6797 (p90) REVERT: B 102 TYR cc_start: 0.9297 (t80) cc_final: 0.8862 (t80) REVERT: C 106 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8140 (ttp-170) outliers start: 12 outliers final: 11 residues processed: 94 average time/residue: 0.1954 time to fit residues: 23.6971 Evaluate side-chains 82 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 155 THR 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: 0.9980 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5952 Z= 0.212 Angle : 0.554 8.504 8187 Z= 0.292 Chirality : 0.045 0.186 948 Planarity : 0.003 0.025 1032 Dihedral : 6.295 81.644 1038 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 0.32 (0.30), residues: 783 helix: 2.02 (0.39), residues: 207 sheet: 0.74 (0.39), residues: 189 loop : -1.11 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.005 0.001 HIS B 295 PHE 0.029 0.002 PHE A 115 TYR 0.024 0.001 TYR C 195 ARG 0.003 0.000 ARG A 117 *********************** 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 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9289 (t80) cc_final: 0.8810 (t80) REVERT: A 106 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.7998 (tmm-80) REVERT: B 82 TYR cc_start: 0.7097 (p90) cc_final: 0.6802 (p90) REVERT: B 102 TYR cc_start: 0.9295 (t80) cc_final: 0.8905 (t80) REVERT: B 106 ARG cc_start: 0.8745 (tmm-80) cc_final: 0.8246 (ttp-110) REVERT: C 106 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8190 (ttp-170) outliers start: 11 outliers final: 11 residues processed: 91 average time/residue: 0.2105 time to fit residues: 24.2728 Evaluate side-chains 78 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 155 THR 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: 0.6980 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5952 Z= 0.188 Angle : 0.555 8.501 8187 Z= 0.289 Chirality : 0.044 0.192 948 Planarity : 0.003 0.025 1032 Dihedral : 6.208 79.564 1038 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.43 % Allowed : 20.09 % Favored : 77.48 % 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: 0.35 (0.31), residues: 783 helix: 2.09 (0.39), residues: 207 sheet: 0.74 (0.39), residues: 189 loop : -1.11 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.005 0.001 HIS B 295 PHE 0.029 0.002 PHE A 115 TYR 0.023 0.001 TYR C 195 ARG 0.003 0.000 ARG A 117 ********************** 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 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.9268 (t80) cc_final: 0.8788 (t80) REVERT: A 106 ARG cc_start: 0.8796 (ttp-110) cc_final: 0.7970 (tmm-80) REVERT: B 82 TYR cc_start: 0.7043 (p90) cc_final: 0.6734 (p90) REVERT: B 102 TYR cc_start: 0.9330 (t80) cc_final: 0.8929 (t80) REVERT: B 106 ARG cc_start: 0.8731 (tmm-80) cc_final: 0.8238 (ttp-110) REVERT: B 255 TRP cc_start: 0.8288 (t60) cc_final: 0.7983 (t60) REVERT: C 66 LEU cc_start: 0.8762 (mp) cc_final: 0.8482 (mt) REVERT: C 106 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8256 (ttp-110) REVERT: C 304 GLU cc_start: 0.8056 (tp30) cc_final: 0.6876 (tp30) outliers start: 11 outliers final: 11 residues processed: 91 average time/residue: 0.2088 time to fit residues: 24.3611 Evaluate side-chains 89 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 155 THR 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 17 optimal weight: 0.0770 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.178134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147087 restraints weight = 8259.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145429 restraints weight = 11764.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.147540 restraints weight = 9196.451| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4740 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= 0.187 Angle : 0.549 8.447 8187 Z= 0.286 Chirality : 0.044 0.188 948 Planarity : 0.003 0.026 1032 Dihedral : 6.111 77.137 1038 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.87 % Allowed : 19.21 % 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: 0.37 (0.31), residues: 783 helix: 2.13 (0.39), residues: 207 sheet: 0.74 (0.39), residues: 189 loop : -1.12 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.005 0.001 HIS B 295 PHE 0.029 0.002 PHE A 115 TYR 0.022 0.001 TYR C 195 ARG 0.003 0.000 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1389.52 seconds wall clock time: 25 minutes 42.41 seconds (1542.41 seconds total)