Starting phenix.real_space_refine on Sun Mar 10 15:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/03_2024/8fa1_28947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/03_2024/8fa1_28947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/03_2024/8fa1_28947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/03_2024/8fa1_28947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/03_2024/8fa1_28947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/03_2024/8fa1_28947.pdb" } resolution = 2.51 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= 0.020 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 1572 2.51 5 N 447 2.21 5 O 534 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-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2553 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 532 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: 1.78, per 1000 atoms: 0.70 Number of scatterers: 2553 At special positions: 0 Unit cell: (47.436, 55.476, 118.992, 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 534 8.00 N 447 7.00 C 1572 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: 1.10 Conformation dependent library (CDL) restraints added in 474.6 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: 0.20 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 removed outlier: 3.776A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.776A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.776A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 232 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: 0.67 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 483 1.29 - 1.35: 417 1.35 - 1.42: 66 1.42 - 1.48: 378 1.48 - 1.54: 1215 Bond restraints: 2559 Sorted by residual: bond pdb=" CA ASN D1178 " pdb=" CB ASN D1178 " ideal model delta sigma weight residual 1.531 1.505 0.025 3.12e-02 1.03e+03 6.58e-01 bond pdb=" CA ASN F1178 " pdb=" CB ASN F1178 " ideal model delta sigma weight residual 1.531 1.505 0.025 3.12e-02 1.03e+03 6.49e-01 bond pdb=" CB VAL E1177 " pdb=" CG2 VAL E1177 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.48e-01 bond pdb=" CB VAL F1177 " pdb=" CG2 VAL F1177 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.42e-01 bond pdb=" CB VAL D1177 " pdb=" CG2 VAL D1177 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.30e-01 ... (remaining 2554 not shown) Histogram of bond angle deviations from ideal: 103.09 - 108.71: 49 108.71 - 114.33: 1616 114.33 - 119.95: 677 119.95 - 125.56: 1105 125.56 - 131.18: 6 Bond angle restraints: 3453 Sorted by residual: angle pdb=" N ASN A 978 " pdb=" CA ASN A 978 " pdb=" CB ASN A 978 " ideal model delta sigma weight residual 110.16 113.84 -3.68 1.48e+00 4.57e-01 6.19e+00 angle pdb=" N ASN B 978 " pdb=" CA ASN B 978 " pdb=" CB ASN B 978 " ideal model delta sigma weight residual 110.16 113.84 -3.68 1.48e+00 4.57e-01 6.18e+00 angle pdb=" N ASN C 978 " pdb=" CA ASN C 978 " pdb=" CB ASN C 978 " ideal model delta sigma weight residual 110.16 113.83 -3.67 1.48e+00 4.57e-01 6.14e+00 angle pdb=" CA LEU B 962 " pdb=" CB LEU B 962 " pdb=" CG LEU B 962 " ideal model delta sigma weight residual 116.30 123.04 -6.74 3.50e+00 8.16e-02 3.71e+00 angle pdb=" CA LEU A 962 " pdb=" CB LEU A 962 " pdb=" CG LEU A 962 " ideal model delta sigma weight residual 116.30 122.99 -6.69 3.50e+00 8.16e-02 3.65e+00 ... (remaining 3448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 1368 14.97 - 29.94: 189 29.94 - 44.91: 21 44.91 - 59.88: 18 59.88 - 74.85: 9 Dihedral angle restraints: 1605 sinusoidal: 624 harmonic: 981 Sorted by residual: dihedral pdb=" N GLN C 957 " pdb=" CA GLN C 957 " pdb=" CB GLN C 957 " pdb=" CG GLN C 957 " ideal model delta sinusoidal sigma weight residual 180.00 -120.29 -59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN B 957 " pdb=" CA GLN B 957 " pdb=" CB GLN B 957 " pdb=" CG GLN B 957 " ideal model delta sinusoidal sigma weight residual -180.00 -120.29 -59.71 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN A 957 " pdb=" CA GLN A 957 " pdb=" CB GLN A 957 " pdb=" CG GLN A 957 " ideal model delta sinusoidal sigma weight residual -180.00 -120.33 -59.67 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 255 0.027 - 0.053: 119 0.053 - 0.080: 36 0.080 - 0.106: 19 0.106 - 0.133: 6 Chirality restraints: 435 Sorted by residual: chirality pdb=" CA GLN A 920 " pdb=" N GLN A 920 " pdb=" C GLN A 920 " pdb=" CB GLN A 920 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA GLN B 920 " pdb=" N GLN B 920 " pdb=" C GLN B 920 " pdb=" CB GLN B 920 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA GLN C 920 " pdb=" N GLN C 920 " pdb=" C GLN C 920 " pdb=" CB GLN C 920 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 432 not shown) Planarity restraints: 453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 919 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C ASN A 919 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN A 919 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A 920 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 919 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C ASN B 919 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN B 919 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN B 920 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 919 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C ASN C 919 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN C 919 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN C 920 " -0.013 2.00e-02 2.50e+03 ... (remaining 450 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 703 2.81 - 3.33: 2762 3.33 - 3.85: 4259 3.85 - 4.38: 4728 4.38 - 4.90: 8073 Nonbonded interactions: 20525 Sorted by model distance: nonbonded pdb=" ND2 ASN C 978 " pdb=" OD1 ASP F1163 " model vdw 2.286 2.520 nonbonded pdb=" ND2 ASN B 978 " pdb=" OD1 ASP E1163 " model vdw 2.333 2.520 nonbonded pdb=" ND2 ASN A 978 " pdb=" OD1 ASP D1163 " model vdw 2.388 2.520 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.418 2.520 nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.429 2.520 ... (remaining 20520 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: 0.700 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: 3.390 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.750 Find NCS groups from input model: 0.160 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.006 0.027 2559 Z= 0.353 Angle : 0.572 6.742 3453 Z= 0.296 Chirality : 0.039 0.133 435 Planarity : 0.004 0.034 453 Dihedral : 15.924 74.850 957 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.42), residues: 327 helix: 1.08 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -1.33 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.003 0.001 PHE A 927 ARG 0.004 0.001 ARG C 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 38 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.285 Fit side-chains REVERT: B 980 ILE cc_start: 0.8929 (mt) cc_final: 0.8713 (mt) REVERT: C 973 ILE cc_start: 0.9020 (mt) cc_final: 0.8778 (mt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.4774 time to fit residues: 19.4172 Evaluate side-chains 37 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 24 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: A 965 GLN E1159 HIS F1159 HIS ** F1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2559 Z= 0.214 Angle : 0.454 7.338 3453 Z= 0.237 Chirality : 0.036 0.122 435 Planarity : 0.002 0.019 453 Dihedral : 3.293 11.537 339 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.03 % Allowed : 15.82 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.45), residues: 327 helix: 3.07 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.56 (0.78), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE C 970 ARG 0.002 0.001 ARG C 983 *********************** 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 47 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.290 Fit side-chains REVERT: C 973 ILE cc_start: 0.9012 (mt) cc_final: 0.8762 (mt) outliers start: 9 outliers final: 1 residues processed: 45 average time/residue: 0.5030 time to fit residues: 24.0327 Evaluate side-chains 39 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1177 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2559 Z= 0.224 Angle : 0.448 7.435 3453 Z= 0.231 Chirality : 0.037 0.134 435 Planarity : 0.002 0.015 453 Dihedral : 3.221 10.094 339 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.36 % Allowed : 17.51 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.45 (0.46), residues: 327 helix: 3.78 (0.28), residues: 252 sheet: None (None), residues: 0 loop : -0.26 (0.83), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.006 0.002 PHE C 970 ARG 0.002 0.001 ARG A 983 *********************** 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 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.304 Fit side-chains REVERT: C 973 ILE cc_start: 0.9013 (mt) cc_final: 0.8762 (mt) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 0.4936 time to fit residues: 21.0272 Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL 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: 3.9990 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 26 optimal weight: 0.0570 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2559 Z= 0.180 Angle : 0.425 7.054 3453 Z= 0.220 Chirality : 0.036 0.130 435 Planarity : 0.002 0.010 453 Dihedral : 3.113 10.625 339 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.36 % Allowed : 17.85 % Favored : 79.80 % 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: 4.96 (0.46), residues: 327 helix: 4.18 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.04 (0.82), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.005 0.001 PHE A 927 ARG 0.002 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 47 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.382 Fit side-chains REVERT: A 962 LEU cc_start: 0.8841 (tm) cc_final: 0.8631 (tt) REVERT: C 973 ILE cc_start: 0.9017 (mt) cc_final: 0.8764 (mt) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.5082 time to fit residues: 23.7809 Evaluate side-chains 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.0010 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 overall best weight: 0.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 HIS ** F1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2559 Z= 0.134 Angle : 0.397 7.052 3453 Z= 0.207 Chirality : 0.035 0.133 435 Planarity : 0.002 0.010 453 Dihedral : 2.950 11.282 339 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.36 % Allowed : 16.84 % Favored : 80.81 % 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: 5.48 (0.46), residues: 327 helix: 4.55 (0.27), residues: 249 sheet: None (None), residues: 0 loop : 0.19 (0.85), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE A 927 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 45 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.309 Fit side-chains REVERT: C 973 ILE cc_start: 0.9019 (mt) cc_final: 0.8770 (mt) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.4864 time to fit residues: 21.2838 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain F residue 1177 VAL 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: 0.4980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 30 optimal weight: 0.0030 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2559 Z= 0.190 Angle : 0.422 6.926 3453 Z= 0.222 Chirality : 0.037 0.130 435 Planarity : 0.002 0.010 453 Dihedral : 3.023 10.690 339 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.36 % Allowed : 17.51 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.24 (0.45), residues: 327 helix: 4.38 (0.27), residues: 249 sheet: None (None), residues: 0 loop : 0.05 (0.83), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.004 0.001 PHE A 927 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 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.295 Fit side-chains REVERT: C 973 ILE cc_start: 0.9008 (mt) cc_final: 0.8751 (mt) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.4787 time to fit residues: 20.9510 Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain E residue 1177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2559 Z= 0.196 Angle : 0.412 7.980 3453 Z= 0.217 Chirality : 0.037 0.126 435 Planarity : 0.002 0.012 453 Dihedral : 3.043 11.643 339 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.68 % Allowed : 17.17 % Favored : 81.14 % 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: 5.18 (0.45), residues: 327 helix: 4.36 (0.27), residues: 249 sheet: None (None), residues: 0 loop : -0.04 (0.82), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D1159 PHE 0.004 0.001 PHE A 927 ARG 0.002 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 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.309 Fit side-chains REVERT: C 973 ILE cc_start: 0.9005 (mt) cc_final: 0.8746 (mt) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.6348 time to fit residues: 27.9789 Evaluate side-chains 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 0.0050 chunk 28 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2559 Z= 0.171 Angle : 0.405 7.593 3453 Z= 0.212 Chirality : 0.036 0.121 435 Planarity : 0.002 0.010 453 Dihedral : 3.016 11.267 339 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.35 % Allowed : 17.51 % Favored : 81.14 % 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: 5.27 (0.45), residues: 327 helix: 4.41 (0.27), residues: 249 sheet: None (None), residues: 0 loop : 0.04 (0.82), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE A 927 ARG 0.001 0.000 ARG B 983 *********************** 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 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.300 Fit side-chains REVERT: C 973 ILE cc_start: 0.9001 (mt) cc_final: 0.8740 (mt) outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 0.5936 time to fit residues: 25.7148 Evaluate side-chains 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 2559 Z= 0.194 Angle : 0.428 7.571 3453 Z= 0.228 Chirality : 0.037 0.171 435 Planarity : 0.002 0.010 453 Dihedral : 3.041 11.549 339 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.35 % Allowed : 17.51 % Favored : 81.14 % 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: 5.23 (0.45), residues: 327 helix: 4.38 (0.27), residues: 249 sheet: None (None), residues: 0 loop : 0.04 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE A 970 ARG 0.002 0.000 ARG A 983 *********************** 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 46 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.296 Fit side-chains REVERT: C 973 ILE cc_start: 0.8996 (mt) cc_final: 0.8734 (mt) outliers start: 4 outliers final: 4 residues processed: 44 average time/residue: 0.5738 time to fit residues: 26.6718 Evaluate side-chains 46 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 2559 Z= 0.179 Angle : 0.443 7.693 3453 Z= 0.235 Chirality : 0.037 0.154 435 Planarity : 0.002 0.020 453 Dihedral : 3.021 11.532 339 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.35 % Allowed : 18.18 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.29 (0.45), residues: 327 helix: 4.42 (0.27), residues: 249 sheet: None (None), residues: 0 loop : 0.07 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.004 0.001 PHE A 970 ARG 0.002 0.000 ARG A 983 ********************** 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 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.296 Fit side-chains REVERT: C 973 ILE cc_start: 0.8999 (mt) cc_final: 0.8735 (mt) outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 0.6011 time to fit residues: 26.0082 Evaluate side-chains 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain E residue 1177 VAL Chi-restraints excluded: chain F residue 1177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** 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 = 0.4390 r_free = 0.4390 target = 0.142667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.124461 restraints weight = 3541.641| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.17 r_work: 0.3932 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2559 Z= 0.216 Angle : 0.454 7.646 3453 Z= 0.240 Chirality : 0.038 0.143 435 Planarity : 0.002 0.010 453 Dihedral : 3.093 11.589 339 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.35 % Allowed : 19.19 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.07 (0.45), residues: 327 helix: 4.27 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.02 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.005 0.001 PHE B 970 ARG 0.001 0.000 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.72 seconds wall clock time: 21 minutes 24.33 seconds (1284.33 seconds total)