Starting phenix.real_space_refine on Thu Dec 7 16:33:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/12_2023/8czi_27098.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/12_2023/8czi_27098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/12_2023/8czi_27098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/12_2023/8czi_27098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/12_2023/8czi_27098.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/12_2023/8czi_27098.pdb" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 3 Type Number sf(0) Gaussians C 1566 2.51 5 N 447 2.21 5 O 537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 531 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "F" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Time building chain proxies: 1.85, per 1000 atoms: 0.73 Number of scatterers: 2550 At special positions: 0 Unit cell: (45.71, 49.7913, 117.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 537 8.00 N 447 7.00 C 1566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 469.6 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 235 hydrogen bonds defined for protein. 696 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: 0.65 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 486 1.29 - 1.35: 420 1.35 - 1.42: 83 1.42 - 1.48: 361 1.48 - 1.54: 1206 Bond restraints: 2556 Sorted by residual: bond pdb=" C ILE E1179 " pdb=" O ILE E1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 5.84e-01 bond pdb=" C ILE D1179 " pdb=" O ILE D1179 " ideal model delta sigma weight residual 1.236 1.227 0.009 1.19e-02 7.06e+03 5.77e-01 bond pdb=" N VAL E1176 " pdb=" CA VAL E1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.77e-01 bond pdb=" N VAL F1176 " pdb=" CA VAL F1176 " ideal model delta sigma weight residual 1.457 1.448 0.009 1.15e-02 7.56e+03 5.75e-01 bond pdb=" N VAL D1176 " pdb=" CA VAL D1176 " ideal model delta sigma weight residual 1.457 1.449 0.008 1.15e-02 7.56e+03 4.95e-01 ... (remaining 2551 not shown) Histogram of bond angle deviations from ideal: 102.83 - 108.50: 36 108.50 - 114.18: 1615 114.18 - 119.85: 614 119.85 - 125.52: 1182 125.52 - 131.20: 6 Bond angle restraints: 3453 Sorted by residual: angle pdb=" C ASP F1165 " pdb=" CA ASP F1165 " pdb=" CB ASP F1165 " ideal model delta sigma weight residual 110.19 111.68 -1.49 1.62e+00 3.81e-01 8.49e-01 angle pdb=" C ASP D1165 " pdb=" CA ASP D1165 " pdb=" CB ASP D1165 " ideal model delta sigma weight residual 110.19 111.67 -1.48 1.62e+00 3.81e-01 8.39e-01 angle pdb=" C ASP E1165 " pdb=" CA ASP E1165 " pdb=" CB ASP E1165 " ideal model delta sigma weight residual 110.19 111.67 -1.48 1.62e+00 3.81e-01 8.35e-01 angle pdb=" CA PRO D1162 " pdb=" CB PRO D1162 " pdb=" CG PRO D1162 " ideal model delta sigma weight residual 104.50 106.22 -1.72 1.90e+00 2.77e-01 8.19e-01 angle pdb=" CA PRO E1162 " pdb=" CB PRO E1162 " pdb=" CG PRO E1162 " ideal model delta sigma weight residual 104.50 106.21 -1.71 1.90e+00 2.77e-01 8.14e-01 ... (remaining 3448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1461 17.82 - 35.64: 114 35.64 - 53.46: 9 53.46 - 71.28: 9 71.28 - 89.10: 6 Dihedral angle restraints: 1599 sinusoidal: 618 harmonic: 981 Sorted by residual: dihedral pdb=" N ASN D1187 " pdb=" CA ASN D1187 " pdb=" CB ASN D1187 " pdb=" CG ASN D1187 " ideal model delta sinusoidal sigma weight residual -60.00 -97.03 37.03 3 1.50e+01 4.44e-03 6.45e+00 dihedral pdb=" N ASN E1187 " pdb=" CA ASN E1187 " pdb=" CB ASN E1187 " pdb=" CG ASN E1187 " ideal model delta sinusoidal sigma weight residual -60.00 -97.02 37.02 3 1.50e+01 4.44e-03 6.44e+00 dihedral pdb=" N ASN F1187 " pdb=" CA ASN F1187 " pdb=" CB ASN F1187 " pdb=" CG ASN F1187 " ideal model delta sinusoidal sigma weight residual -60.00 -97.02 37.02 3 1.50e+01 4.44e-03 6.44e+00 ... (remaining 1596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 214 0.021 - 0.041: 148 0.041 - 0.062: 59 0.062 - 0.083: 2 0.083 - 0.103: 12 Chirality restraints: 435 Sorted by residual: chirality pdb=" CA ILE F1172 " pdb=" N ILE F1172 " pdb=" C ILE F1172 " pdb=" CB ILE F1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.67e-01 chirality pdb=" CA ILE D1172 " pdb=" N ILE D1172 " pdb=" C ILE D1172 " pdb=" CB ILE D1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA ILE E1172 " pdb=" N ILE E1172 " pdb=" C ILE E1172 " pdb=" CB ILE E1172 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.60e-01 ... (remaining 432 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D1161 " -0.012 5.00e-02 4.00e+02 1.79e-02 5.13e-01 pdb=" N PRO D1162 " 0.031 5.00e-02 4.00e+02 pdb=" CA PRO D1162 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO D1162 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F1161 " 0.012 5.00e-02 4.00e+02 1.78e-02 5.09e-01 pdb=" N PRO F1162 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO F1162 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO F1162 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E1161 " 0.012 5.00e-02 4.00e+02 1.76e-02 4.97e-01 pdb=" N PRO E1162 " -0.030 5.00e-02 4.00e+02 pdb=" CA PRO E1162 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO E1162 " 0.010 5.00e-02 4.00e+02 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 903 2.89 - 3.39: 2866 3.39 - 3.89: 4324 3.89 - 4.40: 4612 4.40 - 4.90: 7926 Nonbonded interactions: 20631 Sorted by model distance: nonbonded pdb=" ND2 ASN C 978 " pdb=" OD1 ASP F1163 " model vdw 2.382 2.520 nonbonded pdb=" ND2 ASN A 978 " pdb=" OD1 ASP D1163 " model vdw 2.383 2.520 nonbonded pdb=" ND2 ASN B 978 " pdb=" OD1 ASP E1163 " model vdw 2.384 2.520 nonbonded pdb=" NE2 GLN B 935 " pdb=" O ALA E1190 " model vdw 2.396 2.520 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.397 2.520 ... (remaining 20626 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.740 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: 3.390 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.030 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2556 Z= 0.276 Angle : 0.333 2.918 3453 Z= 0.199 Chirality : 0.031 0.103 435 Planarity : 0.002 0.018 456 Dihedral : 14.483 89.102 951 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.41), residues: 327 helix: 3.03 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -1.90 (0.56), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.007 0.001 PHE A 970 ARG 0.001 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.286 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.4361 time to fit residues: 13.7247 Evaluate side-chains 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2556 Z= 0.260 Angle : 0.333 2.996 3453 Z= 0.190 Chirality : 0.033 0.097 435 Planarity : 0.002 0.018 456 Dihedral : 2.921 10.211 339 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 4.71 % Favored : 94.61 % 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: 4.46 (0.42), residues: 327 helix: 4.25 (0.26), residues: 243 sheet: None (None), residues: 0 loop : -1.40 (0.58), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.007 0.001 PHE C 970 ARG 0.001 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.218 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.3004 time to fit residues: 9.4149 Evaluate side-chains 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.0000 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 overall best weight: 0.3942 ------------------------------------------------------------------------------- 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: 0.7602 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2556 Z= 0.168 Angle : 0.289 3.432 3453 Z= 0.169 Chirality : 0.031 0.102 435 Planarity : 0.002 0.017 456 Dihedral : 2.668 9.933 339 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 5.39 % Favored : 93.60 % 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: 5.43 (0.43), residues: 327 helix: 4.95 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -1.04 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.006 0.001 PHE A 970 ARG 0.000 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.298 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.2492 time to fit residues: 8.1160 Evaluate side-chains 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0287 time to fit residues: 0.4813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2556 Z= 0.249 Angle : 0.327 3.432 3453 Z= 0.185 Chirality : 0.033 0.103 435 Planarity : 0.002 0.018 456 Dihedral : 2.806 10.472 339 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 5.39 % Favored : 93.27 % 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: 5.35 (0.42), residues: 327 helix: 4.87 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.97 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.307 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.2919 time to fit residues: 10.2332 Evaluate side-chains 34 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0810 time to fit residues: 0.7426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2556 Z= 0.211 Angle : 0.317 3.235 3453 Z= 0.181 Chirality : 0.032 0.104 435 Planarity : 0.002 0.019 456 Dihedral : 2.743 10.301 339 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 6.40 % Favored : 92.26 % 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: 5.44 (0.42), residues: 327 helix: 4.90 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.83 (0.64), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.279 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.2337 time to fit residues: 7.6024 Evaluate side-chains 31 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0861 time to fit residues: 0.7413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2556 Z= 0.242 Angle : 0.344 4.160 3453 Z= 0.187 Chirality : 0.033 0.104 435 Planarity : 0.002 0.019 456 Dihedral : 2.793 10.501 339 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 6.40 % Favored : 92.26 % 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: 5.42 (0.42), residues: 327 helix: 4.86 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.74 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.287 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.2255 time to fit residues: 7.8808 Evaluate side-chains 34 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0728 time to fit residues: 0.7756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2556 Z= 0.168 Angle : 0.318 4.079 3453 Z= 0.176 Chirality : 0.032 0.104 435 Planarity : 0.001 0.016 456 Dihedral : 2.636 10.234 339 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 8.42 % Favored : 91.25 % 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: 5.74 (0.42), residues: 327 helix: 5.10 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.65 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.003 0.001 PHE C 970 ARG 0.000 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.256 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.2158 time to fit residues: 7.5464 Evaluate side-chains 31 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0748 time to fit residues: 0.4967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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: 0.7610 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2556 Z= 0.191 Angle : 0.341 5.885 3453 Z= 0.181 Chirality : 0.032 0.104 435 Planarity : 0.002 0.017 456 Dihedral : 2.665 10.404 339 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 8.08 % Favored : 90.91 % 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: 5.74 (0.43), residues: 327 helix: 5.08 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.59 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE C 970 ARG 0.000 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.284 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.2116 time to fit residues: 7.2202 Evaluate side-chains 32 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0600 time to fit residues: 0.6594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2556 Z= 0.187 Angle : 0.328 4.911 3453 Z= 0.175 Chirality : 0.032 0.104 435 Planarity : 0.002 0.016 456 Dihedral : 2.649 10.595 339 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 8.42 % Favored : 91.25 % 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: 5.78 (0.43), residues: 327 helix: 5.11 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.58 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE A 970 ARG 0.001 0.000 ARG D1185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.284 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.2121 time to fit residues: 7.2200 Evaluate side-chains 30 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0756 time to fit residues: 0.5053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.7608 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2556 Z= 0.188 Angle : 0.336 4.584 3453 Z= 0.185 Chirality : 0.032 0.104 435 Planarity : 0.002 0.016 456 Dihedral : 2.635 10.388 339 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % 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: 5.78 (0.43), residues: 327 helix: 5.12 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -0.59 (0.68), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE C 970 ARG 0.000 0.000 ARG D1185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.405 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2340 time to fit residues: 7.6798 Evaluate side-chains 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.140166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.123763 restraints weight = 3279.713| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.58 r_work: 0.3796 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2556 Z= 0.237 Angle : 0.352 4.500 3453 Z= 0.193 Chirality : 0.033 0.104 435 Planarity : 0.002 0.018 456 Dihedral : 2.739 10.877 339 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 8.08 % Favored : 91.58 % 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: 5.55 (0.43), residues: 327 helix: 4.93 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.61 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.000 0.000 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1056.78 seconds wall clock time: 19 minutes 41.68 seconds (1181.68 seconds total)