Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:53:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/11_2022/8czi_27098.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/11_2022/8czi_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_27098/11_2022/8czi_27098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/11_2022/8czi_27098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/11_2022/8czi_27098.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czi_27098/11_2022/8czi_27098.pdb" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4778/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: 2.34, per 1000 atoms: 0.92 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: 1.09 Conformation dependent library (CDL) restraints added in 383.1 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: 0.06 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: 0.70 Time building geometry restraints manager: 1.18 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 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. 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: 0.690 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: 3.450 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.810 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 % 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 *********************** 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 : 0.297 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.4488 time to fit residues: 14.1293 Evaluate side-chains 27 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4351 ------------------------------------------------------------------------------- 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: 0.6980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8064 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 2556 Z= 0.253 Angle : 0.327 2.977 3453 Z= 0.188 Chirality : 0.032 0.097 435 Planarity : 0.002 0.018 456 Dihedral : 2.894 10.178 339 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.01 % 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 : -1.41 (0.58), residues: 84 *********************** 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 31 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.235 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.3413 time to fit residues: 10.7834 Evaluate side-chains 29 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0865 time to fit residues: 0.5703 ------------------------------------------------------------------------------- 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: 0.8980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.0060 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 0.0370 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.2552 ------------------------------------------------------------------------------- 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: 0.8035 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 2556 Z= 0.131 Angle : 0.278 3.366 3453 Z= 0.163 Chirality : 0.031 0.102 435 Planarity : 0.002 0.016 456 Dihedral : 2.587 9.637 339 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.63 (0.43), residues: 327 helix: 5.11 (0.24), residues: 243 sheet: None (None), residues: 0 loop : -1.04 (0.63), residues: 84 *********************** 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 30 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.312 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.2924 time to fit residues: 8.7875 Evaluate side-chains 28 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0427 time to fit residues: 0.6098 ------------------------------------------------------------------------------- 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: 0.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8065 moved from start: 0.1459 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= 0.244 Angle : 0.328 3.438 3453 Z= 0.187 Chirality : 0.034 0.172 435 Planarity : 0.002 0.018 456 Dihedral : 2.792 10.269 339 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.01 % 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 (0.43), residues: 327 helix: 4.93 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.97 (0.63), residues: 84 *********************** 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 33 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.272 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.2745 time to fit residues: 9.3618 Evaluate side-chains 32 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0903 time to fit residues: 0.6033 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8063 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 2556 Z= 0.223 Angle : 0.320 3.277 3453 Z= 0.183 Chirality : 0.034 0.166 435 Planarity : 0.002 0.019 456 Dihedral : 2.760 10.227 339 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.41 (0.42), residues: 327 helix: 4.89 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.86 (0.64), residues: 84 *********************** 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 35 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.252 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.2039 time to fit residues: 7.1830 Evaluate side-chains 33 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0900 time to fit residues: 0.8568 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.1658 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= 0.204 Angle : 0.330 4.019 3453 Z= 0.181 Chirality : 0.033 0.166 435 Planarity : 0.002 0.019 456 Dihedral : 2.702 10.331 339 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.01 % 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: 5.60 (0.43), residues: 327 helix: 5.00 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.72 (0.65), residues: 84 *********************** 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 33 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.297 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 30 average time/residue: 0.2174 time to fit residues: 7.7303 Evaluate side-chains 32 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1151 time to fit residues: 1.0241 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1717 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= 0.217 Angle : 0.348 4.990 3453 Z= 0.187 Chirality : 0.034 0.169 435 Planarity : 0.002 0.017 456 Dihedral : 2.726 10.378 339 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.53 (0.43), residues: 327 helix: 4.94 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.71 (0.66), residues: 84 *********************** 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 32 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.302 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.1993 time to fit residues: 7.3126 Evaluate side-chains 30 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0260 time to fit residues: 0.4730 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.004 0.021 2556 Z= 0.277 Angle : 0.377 5.425 3453 Z= 0.201 Chirality : 0.035 0.183 435 Planarity : 0.002 0.019 456 Dihedral : 2.864 10.768 339 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.28 (0.43), residues: 327 helix: 4.74 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.71 (0.66), residues: 84 *********************** 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 34 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.242 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.2200 time to fit residues: 7.8918 Evaluate side-chains 33 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.420 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0695 time to fit residues: 0.8158 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 0.0070 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1798 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= 0.200 Angle : 0.338 4.593 3453 Z= 0.182 Chirality : 0.033 0.175 435 Planarity : 0.002 0.016 456 Dihedral : 2.710 10.591 339 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % 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: 5.58 (0.43), residues: 327 helix: 4.96 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.64 (0.66), residues: 84 *********************** 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: 0 poor density : 30 time to evaluate : 0.299 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2083 time to fit residues: 7.3509 Evaluate side-chains 30 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4242 ------------------------------------------------------------------------------- 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: 0.5980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1826 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= 0.195 Angle : 0.345 4.652 3453 Z= 0.191 Chirality : 0.033 0.175 435 Planarity : 0.002 0.017 456 Dihedral : 2.677 10.288 339 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % 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: 5.64 (0.43), residues: 327 helix: 5.00 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.61 (0.67), residues: 84 ********************** 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 30 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.294 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2111 time to fit residues: 7.4308 Evaluate side-chains 30 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4035 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.139951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.123548 restraints weight = 3278.439| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.57 r_work: 0.3914 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.3885 rms_B_bonded: 1.48 restraints_weight: 0.1250 r_work: 0.3869 rms_B_bonded: 1.62 restraints_weight: 0.0625 r_work: 0.3851 rms_B_bonded: 1.81 restraints_weight: 0.0312 r_work: 0.3831 rms_B_bonded: 2.05 restraints_weight: 0.0156 r_work: 0.3809 rms_B_bonded: 2.35 restraints_weight: 0.0078 r_work: 0.3784 rms_B_bonded: 2.70 restraints_weight: 0.0039 r_work: 0.3756 rms_B_bonded: 3.12 restraints_weight: 0.0020 r_work: 0.3723 rms_B_bonded: 3.63 restraints_weight: 0.0010 r_work: 0.3684 rms_B_bonded: 4.22 restraints_weight: 0.0005 r_work: 0.3639 rms_B_bonded: 4.94 restraints_weight: 0.0002 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1849 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= 0.265 Angle : 0.369 4.579 3453 Z= 0.203 Chirality : 0.034 0.186 435 Planarity : 0.002 0.018 456 Dihedral : 2.809 10.622 339 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % 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: 5.34 (0.43), residues: 327 helix: 4.77 (0.25), residues: 243 sheet: None (None), residues: 0 loop : -0.65 (0.67), residues: 84 =============================================================================== Job complete usr+sys time: 934.83 seconds wall clock time: 18 minutes 13.63 seconds (1093.63 seconds total)