Starting phenix.real_space_refine on Mon Nov 13 20:35:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/11_2023/7qbi_13887.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/11_2023/7qbi_13887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/11_2023/7qbi_13887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/11_2023/7qbi_13887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/11_2023/7qbi_13887.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbi_13887/11_2023/7qbi_13887.pdb" } resolution = 3.46 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= 0.002 sd= 0.093 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 20 5.16 5 C 3360 2.51 5 N 718 2.21 5 O 898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 4996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2140 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "K" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "B" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2140 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'NAG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'NAG': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.42, per 1000 atoms: 0.68 Number of scatterers: 4996 At special positions: 0 Unit cell: (75.9, 73.7, 94.6, 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 20 16.00 O 898 8.00 N 718 7.00 C 3360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 32 " " NAG B 502 " - " ASN B 25 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 935.0 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 78.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 18 through 21 removed outlier: 3.827A pdb=" N GLN A 21 " --> pdb=" O ASN A 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 21' Processing helix chain 'A' and resid 38 through 73 Processing helix chain 'A' and resid 78 through 102 Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 121 through 154 removed outlier: 3.522A pdb=" N VAL A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 195 removed outlier: 3.921A pdb=" N VAL A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 236 removed outlier: 3.678A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 268 removed outlier: 3.581A pdb=" N ILE A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 301 removed outlier: 3.801A pdb=" N VAL A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 18 through 21 removed outlier: 3.827A pdb=" N GLN B 21 " --> pdb=" O ASN B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 21' Processing helix chain 'B' and resid 38 through 73 Processing helix chain 'B' and resid 78 through 102 Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 121 through 154 removed outlier: 3.522A pdb=" N VAL B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 195 removed outlier: 3.921A pdb=" N VAL B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 236 removed outlier: 3.678A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 268 removed outlier: 3.600A pdb=" N ILE B 246 " --> pdb=" O ASP B 242 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 301 removed outlier: 3.801A pdb=" N VAL B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Proline residue: B 290 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 24 372 hydrogen bonds defined for protein. 1086 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: 1.35 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 734 1.31 - 1.44: 1298 1.44 - 1.57: 3052 1.57 - 1.69: 6 1.69 - 1.82: 36 Bond restraints: 5126 Sorted by residual: bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 5121 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 154 106.15 - 113.14: 3021 113.14 - 120.12: 1952 120.12 - 127.10: 1921 127.10 - 134.08: 44 Bond angle restraints: 7092 Sorted by residual: angle pdb=" N PHE B 244 " pdb=" CA PHE B 244 " pdb=" C PHE B 244 " ideal model delta sigma weight residual 111.33 104.11 7.22 1.21e+00 6.83e-01 3.56e+01 angle pdb=" N PHE A 244 " pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 111.33 104.51 6.82 1.21e+00 6.83e-01 3.18e+01 angle pdb=" C SER A 104 " pdb=" CA SER A 104 " pdb=" CB SER A 104 " ideal model delta sigma weight residual 114.40 108.58 5.82 1.25e+00 6.40e-01 2.17e+01 angle pdb=" C SER B 104 " pdb=" CA SER B 104 " pdb=" CB SER B 104 " ideal model delta sigma weight residual 114.40 108.63 5.77 1.25e+00 6.40e-01 2.13e+01 angle pdb=" N TRP A 70 " pdb=" CA TRP A 70 " pdb=" C TRP A 70 " ideal model delta sigma weight residual 111.03 106.31 4.72 1.11e+00 8.12e-01 1.81e+01 ... (remaining 7087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 2567 17.33 - 34.65: 194 34.65 - 51.98: 58 51.98 - 69.31: 11 69.31 - 86.64: 8 Dihedral angle restraints: 2838 sinusoidal: 1012 harmonic: 1826 Sorted by residual: dihedral pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " pdb=" NE ARG A 74 " pdb=" CZ ARG A 74 " ideal model delta sinusoidal sigma weight residual -180.00 -135.05 -44.95 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG B 74 " pdb=" CD ARG B 74 " pdb=" NE ARG B 74 " pdb=" CZ ARG B 74 " ideal model delta sinusoidal sigma weight residual -180.00 -135.06 -44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB MET A 54 " pdb=" CG MET A 54 " pdb=" SD MET A 54 " pdb=" CE MET A 54 " ideal model delta sinusoidal sigma weight residual -180.00 -120.11 -59.89 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 738 0.061 - 0.122: 156 0.122 - 0.183: 20 0.183 - 0.244: 8 0.244 - 0.305: 2 Chirality restraints: 924 Sorted by residual: chirality pdb=" CA LEU B 236 " pdb=" N LEU B 236 " pdb=" C LEU B 236 " pdb=" CB LEU B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LEU A 236 " pdb=" N LEU A 236 " pdb=" C LEU A 236 " pdb=" CB LEU A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA PHE B 244 " pdb=" N PHE B 244 " pdb=" C PHE B 244 " pdb=" CB PHE B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 921 not shown) Planarity restraints: 804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 219 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C SER A 219 " -0.072 2.00e-02 2.50e+03 pdb=" O SER A 219 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE A 220 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 219 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C SER B 219 " 0.069 2.00e-02 2.50e+03 pdb=" O SER B 219 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE B 220 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 74 " -0.275 9.50e-02 1.11e+02 1.23e-01 9.48e+00 pdb=" NE ARG A 74 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 74 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 74 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 74 " -0.008 2.00e-02 2.50e+03 ... (remaining 801 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 903 2.77 - 3.30: 5100 3.30 - 3.83: 8016 3.83 - 4.37: 9430 4.37 - 4.90: 16177 Nonbonded interactions: 39626 Sorted by model distance: nonbonded pdb=" OE1 GLN B 51 " pdb=" OH TYR B 98 " model vdw 2.231 2.440 nonbonded pdb=" OE1 GLN A 51 " pdb=" OH TYR A 98 " model vdw 2.232 2.440 nonbonded pdb=" O ARG B 122 " pdb=" ND1 HIS B 126 " model vdw 2.296 2.520 nonbonded pdb=" O ARG A 122 " pdb=" ND1 HIS A 126 " model vdw 2.297 2.520 nonbonded pdb=" NH2 ARG A 74 " pdb=" O ALA B 298 " model vdw 2.330 2.520 ... (remaining 39621 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' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.080 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.400 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.008 0.109 5126 Z= 0.532 Angle : 1.064 10.390 7092 Z= 0.600 Chirality : 0.053 0.305 924 Planarity : 0.009 0.123 800 Dihedral : 14.724 86.636 1658 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.31), residues: 614 helix: -0.82 (0.22), residues: 444 sheet: None (None), residues: 0 loop : -0.86 (0.48), residues: 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.500 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1507 time to fit residues: 22.5656 Evaluate side-chains 104 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0020 chunk 45 optimal weight: 0.0010 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN I 2 HIS K 2 HIS B 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5126 Z= 0.192 Angle : 0.562 6.933 7092 Z= 0.275 Chirality : 0.036 0.130 924 Planarity : 0.003 0.021 800 Dihedral : 9.385 73.953 812 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.33), residues: 614 helix: 1.58 (0.23), residues: 446 sheet: None (None), residues: 0 loop : -0.10 (0.50), residues: 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.501 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1563 time to fit residues: 20.6674 Evaluate side-chains 101 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.7693 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 5126 Z= 0.409 Angle : 0.737 9.077 7092 Z= 0.340 Chirality : 0.041 0.154 924 Planarity : 0.003 0.031 800 Dihedral : 9.803 76.734 812 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.84 % Allowed : 13.54 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.33), residues: 614 helix: 2.04 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -0.60 (0.45), residues: 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.520 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 107 average time/residue: 0.1544 time to fit residues: 21.6122 Evaluate side-chains 105 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0513 time to fit residues: 1.2083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7624 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5126 Z= 0.214 Angle : 0.571 6.776 7092 Z= 0.272 Chirality : 0.036 0.134 924 Planarity : 0.003 0.025 800 Dihedral : 9.349 74.277 812 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.75 % Allowed : 17.25 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.34), residues: 614 helix: 2.66 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -0.53 (0.45), residues: 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.471 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 101 average time/residue: 0.1479 time to fit residues: 19.5571 Evaluate side-chains 93 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.461 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0467 time to fit residues: 0.6892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5126 Z= 0.291 Angle : 0.634 7.648 7092 Z= 0.294 Chirality : 0.038 0.138 924 Planarity : 0.003 0.028 800 Dihedral : 9.820 75.578 812 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.40 % Allowed : 19.65 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.34), residues: 614 helix: 2.40 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -0.45 (0.48), residues: 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.539 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.1583 time to fit residues: 20.7809 Evaluate side-chains 101 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0511 time to fit residues: 1.4559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7643 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5126 Z= 0.227 Angle : 0.575 8.286 7092 Z= 0.272 Chirality : 0.037 0.134 924 Planarity : 0.003 0.027 800 Dihedral : 9.672 74.566 812 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.87 % Allowed : 19.43 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.34), residues: 614 helix: 2.81 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -0.41 (0.46), residues: 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.534 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 101 average time/residue: 0.1602 time to fit residues: 21.1714 Evaluate side-chains 97 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0830 time to fit residues: 0.8463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5126 Z= 0.216 Angle : 0.567 6.823 7092 Z= 0.270 Chirality : 0.037 0.135 924 Planarity : 0.003 0.025 800 Dihedral : 9.598 74.344 812 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.75 % Allowed : 20.96 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.34), residues: 614 helix: 2.88 (0.24), residues: 434 sheet: None (None), residues: 0 loop : -0.33 (0.47), residues: 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.516 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 107 average time/residue: 0.1538 time to fit residues: 21.5229 Evaluate side-chains 102 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0546 time to fit residues: 1.1755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7641 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5126 Z= 0.216 Angle : 0.567 6.793 7092 Z= 0.270 Chirality : 0.037 0.137 924 Planarity : 0.003 0.027 800 Dihedral : 9.604 74.299 812 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.87 % Allowed : 20.74 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.33), residues: 614 helix: 2.94 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.33 (0.46), residues: 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.554 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 103 average time/residue: 0.1576 time to fit residues: 21.2781 Evaluate side-chains 98 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0496 time to fit residues: 0.8869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7655 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5126 Z= 0.238 Angle : 0.585 6.876 7092 Z= 0.279 Chirality : 0.037 0.136 924 Planarity : 0.003 0.026 800 Dihedral : 9.759 74.827 812 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.44 % Allowed : 21.83 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.33), residues: 614 helix: 2.92 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.38 (0.45), residues: 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.1593 time to fit residues: 20.5855 Evaluate side-chains 96 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5126 Z= 0.264 Angle : 0.609 6.810 7092 Z= 0.288 Chirality : 0.038 0.137 924 Planarity : 0.003 0.027 800 Dihedral : 9.916 75.457 812 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.44 % Allowed : 22.27 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.33), residues: 614 helix: 2.66 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -0.33 (0.47), residues: 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 97 average time/residue: 0.1558 time to fit residues: 19.6548 Evaluate side-chains 99 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0626 time to fit residues: 0.8313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.177579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137311 restraints weight = 6475.126| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.44 r_work: 0.3437 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5126 Z= 0.219 Angle : 0.575 6.572 7092 Z= 0.276 Chirality : 0.037 0.136 924 Planarity : 0.003 0.027 800 Dihedral : 9.743 74.480 812 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.22 % Allowed : 22.05 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.33), residues: 614 helix: 2.95 (0.23), residues: 434 sheet: None (None), residues: 0 loop : -0.35 (0.46), residues: 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1281.42 seconds wall clock time: 24 minutes 3.61 seconds (1443.61 seconds total)