Starting phenix.real_space_refine on Sun Mar 10 15:02:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/03_2024/7tik_25912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/03_2024/7tik_25912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/03_2024/7tik_25912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/03_2024/7tik_25912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/03_2024/7tik_25912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/03_2024/7tik_25912.pdb" } resolution = 2.4 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 1584 2.51 5 N 450 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 2565 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 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: 1.73, per 1000 atoms: 0.67 Number of scatterers: 2565 At special positions: 0 Unit cell: (52, 42.25, 118.625, 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 531 8.00 N 450 7.00 C 1584 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 464.9 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 removed outlier: 3.618A 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: 3.618A 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: 3.618A 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: 0.69 Time building geometry restraints manager: 1.14 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: 480 1.29 - 1.35: 420 1.35 - 1.41: 89 1.41 - 1.48: 382 1.48 - 1.54: 1206 Bond restraints: 2577 Sorted by residual: bond pdb=" CA LEU C 966 " pdb=" C LEU C 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.44e-01 bond pdb=" CA LEU B 966 " pdb=" C LEU B 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.25e-01 bond pdb=" CB ASN C 955 " pdb=" CG ASN C 955 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 8.08e-01 bond pdb=" CA LEU A 966 " pdb=" C LEU A 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.00e-01 bond pdb=" CA LEU B 962 " pdb=" C LEU B 962 " ideal model delta sigma weight residual 1.524 1.512 0.011 1.29e-02 6.01e+03 7.82e-01 ... (remaining 2572 not shown) Histogram of bond angle deviations from ideal: 103.19 - 108.80: 64 108.80 - 114.42: 1608 114.42 - 120.03: 744 120.03 - 125.65: 1052 125.65 - 131.27: 9 Bond angle restraints: 3477 Sorted by residual: angle pdb=" CA ILE B 980 " pdb=" CB ILE B 980 " pdb=" CG1 ILE B 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.59e+00 angle pdb=" CA ILE A 980 " pdb=" CB ILE A 980 " pdb=" CG1 ILE A 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.56e+00 angle pdb=" CA ILE C 980 " pdb=" CB ILE C 980 " pdb=" CG1 ILE C 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.56e+00 angle pdb=" C ASP C 979 " pdb=" N ILE C 980 " pdb=" CA ILE C 980 " ideal model delta sigma weight residual 120.64 115.62 5.02 1.64e+00 3.72e-01 9.39e+00 angle pdb=" C ASP B 979 " pdb=" N ILE B 980 " pdb=" CA ILE B 980 " ideal model delta sigma weight residual 120.64 115.64 5.00 1.64e+00 3.72e-01 9.29e+00 ... (remaining 3472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1404 17.40 - 34.81: 159 34.81 - 52.21: 21 52.21 - 69.61: 12 69.61 - 87.02: 6 Dihedral angle restraints: 1602 sinusoidal: 621 harmonic: 981 Sorted by residual: dihedral pdb=" CA ASN F1192 " pdb=" CB ASN F1192 " pdb=" CG ASN F1192 " pdb=" OD1 ASN F1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.29 -71.71 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN D1192 " pdb=" CB ASN D1192 " pdb=" CG ASN D1192 " pdb=" OD1 ASN D1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.31 -71.69 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN E1192 " pdb=" CB ASN E1192 " pdb=" CG ASN E1192 " pdb=" OD1 ASN E1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.33 -71.67 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 1599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 210 0.028 - 0.056: 165 0.056 - 0.084: 33 0.084 - 0.112: 7 0.112 - 0.140: 17 Chirality restraints: 432 Sorted by residual: chirality pdb=" CB ILE B 980 " pdb=" CA ILE B 980 " pdb=" CG1 ILE B 980 " pdb=" CG2 ILE B 980 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CB ILE A 980 " pdb=" CA ILE A 980 " pdb=" CG1 ILE A 980 " pdb=" CG2 ILE A 980 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL E1176 " pdb=" N VAL E1176 " pdb=" C VAL E1176 " pdb=" CB VAL E1176 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 429 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 981 " 0.007 2.00e-02 2.50e+03 9.97e-03 1.74e+00 pdb=" CG PHE A 981 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 981 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 981 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 981 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 981 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 981 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 981 " -0.007 2.00e-02 2.50e+03 9.81e-03 1.68e+00 pdb=" CG PHE B 981 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 981 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 981 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 981 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 981 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 981 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 981 " -0.007 2.00e-02 2.50e+03 9.74e-03 1.66e+00 pdb=" CG PHE C 981 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 981 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 981 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 981 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 981 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 981 " -0.000 2.00e-02 2.50e+03 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 463 2.75 - 3.29: 2698 3.29 - 3.83: 4418 3.83 - 4.36: 4841 4.36 - 4.90: 8357 Nonbonded interactions: 20777 Sorted by model distance: nonbonded pdb=" OG SER A 943 " pdb=" OE2 GLU F1182 " model vdw 2.218 2.440 nonbonded pdb=" OD2 ASP A 936 " pdb=" NH2 ARG F1185 " model vdw 2.259 2.520 nonbonded pdb=" O LYS B 964 " pdb=" OG SER B 967 " model vdw 2.283 2.440 nonbonded pdb=" O LYS A 964 " pdb=" OG SER A 967 " model vdw 2.283 2.440 nonbonded pdb=" O LYS C 964 " pdb=" OG SER C 967 " model vdw 2.283 2.440 ... (remaining 20772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.390 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.760 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.007 0.027 2577 Z= 0.418 Angle : 0.491 5.265 3477 Z= 0.283 Chirality : 0.042 0.140 432 Planarity : 0.003 0.016 456 Dihedral : 16.305 87.018 954 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.41), residues: 327 helix: 1.84 (0.28), residues: 252 sheet: None (None), residues: 0 loop : -2.67 (0.54), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 954 PHE 0.023 0.003 PHE A 981 ARG 0.006 0.002 ARG D1185 *********************** 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 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.308 Fit side-chains REVERT: C 969 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8456 (mmtp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.5845 time to fit residues: 33.1694 Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 0.5980 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN B 960 ASN C 960 ASN D1192 ASN E1192 ASN F1192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2577 Z= 0.209 Angle : 0.394 6.155 3477 Z= 0.213 Chirality : 0.038 0.134 432 Planarity : 0.002 0.010 456 Dihedral : 3.295 13.214 339 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.68 % Allowed : 15.15 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.27 (0.43), residues: 327 helix: 3.85 (0.28), residues: 252 sheet: None (None), residues: 0 loop : -1.13 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.015 0.002 PHE A 981 ARG 0.002 0.001 ARG F1185 *********************** 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 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.306 Fit side-chains REVERT: C 963 VAL cc_start: 0.9071 (t) cc_final: 0.8866 (p) REVERT: C 969 LYS cc_start: 0.8713 (mmtp) cc_final: 0.8445 (mmtp) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.5970 time to fit residues: 33.2083 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain E residue 1176 VAL Chi-restraints excluded: chain F residue 1176 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 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 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2577 Z= 0.193 Angle : 0.347 3.992 3477 Z= 0.194 Chirality : 0.036 0.132 432 Planarity : 0.002 0.009 456 Dihedral : 3.071 12.473 339 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.35 % Allowed : 15.82 % Favored : 82.83 % 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: 5.25 (0.44), residues: 327 helix: 4.56 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.84 (0.71), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.010 0.001 PHE A 981 ARG 0.003 0.001 ARG B 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 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 981 PHE cc_start: 0.7884 (m-10) cc_final: 0.7581 (m-80) REVERT: C 963 VAL cc_start: 0.9074 (t) cc_final: 0.8849 (m) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.6156 time to fit residues: 33.0155 Evaluate side-chains 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain E residue 1176 VAL Chi-restraints excluded: chain F residue 1176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN B 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2577 Z= 0.205 Angle : 0.373 5.623 3477 Z= 0.200 Chirality : 0.036 0.137 432 Planarity : 0.001 0.009 456 Dihedral : 3.084 12.458 339 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.02 % Allowed : 14.81 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.52 (0.44), residues: 327 helix: 4.73 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.67 (0.73), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.008 0.001 PHE B 981 ARG 0.003 0.001 ARG B 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 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 977 LEU cc_start: 0.8330 (mt) cc_final: 0.7694 (mt) REVERT: B 981 PHE cc_start: 0.7909 (m-10) cc_final: 0.7666 (m-80) REVERT: C 957 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7969 (mm-40) REVERT: C 963 VAL cc_start: 0.9037 (t) cc_final: 0.8789 (m) REVERT: C 983 ARG cc_start: 0.7586 (mtp180) cc_final: 0.7376 (ttp-170) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.6111 time to fit residues: 33.3299 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain E residue 1176 VAL Chi-restraints excluded: chain F residue 1176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2577 Z= 0.217 Angle : 0.358 4.745 3477 Z= 0.200 Chirality : 0.037 0.132 432 Planarity : 0.002 0.012 456 Dihedral : 3.066 12.562 339 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.69 % Allowed : 13.80 % Favored : 83.50 % 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: 5.57 (0.44), residues: 327 helix: 4.76 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.60 (0.74), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.008 0.001 PHE A 981 ARG 0.003 0.001 ARG B 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 58 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 977 LEU cc_start: 0.8377 (mt) cc_final: 0.7780 (mt) REVERT: B 981 PHE cc_start: 0.7911 (m-10) cc_final: 0.7675 (m-80) REVERT: C 931 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7974 (mp) REVERT: C 957 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7974 (mm-40) REVERT: C 963 VAL cc_start: 0.9051 (t) cc_final: 0.8834 (m) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.5739 time to fit residues: 32.5781 Evaluate side-chains 56 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain E residue 1176 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: 0.0980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2577 Z= 0.183 Angle : 0.378 6.756 3477 Z= 0.201 Chirality : 0.037 0.137 432 Planarity : 0.001 0.010 456 Dihedral : 3.011 12.976 339 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.02 % Allowed : 15.49 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.78 (0.44), residues: 327 helix: 4.88 (0.26), residues: 252 sheet: None (None), residues: 0 loop : -0.44 (0.74), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.008 0.001 PHE B 981 ARG 0.002 0.001 ARG B 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 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7931 (m-10) cc_final: 0.7645 (m-10) REVERT: B 977 LEU cc_start: 0.8377 (mt) cc_final: 0.7808 (mt) REVERT: B 981 PHE cc_start: 0.7900 (m-10) cc_final: 0.7667 (m-80) REVERT: C 957 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7958 (mm-40) REVERT: C 963 VAL cc_start: 0.9039 (t) cc_final: 0.8811 (m) REVERT: C 983 ARG cc_start: 0.7570 (mtp180) cc_final: 0.7361 (ttp-170) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.6290 time to fit residues: 32.9468 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2577 Z= 0.224 Angle : 0.371 5.137 3477 Z= 0.205 Chirality : 0.037 0.143 432 Planarity : 0.002 0.010 456 Dihedral : 3.085 13.899 339 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.02 % Allowed : 15.15 % Favored : 82.83 % 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: 5.70 (0.44), residues: 327 helix: 4.79 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.31 (0.76), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.008 0.001 PHE B 981 ARG 0.002 0.001 ARG B 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 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7954 (m-10) cc_final: 0.7687 (m-80) REVERT: B 977 LEU cc_start: 0.8404 (mt) cc_final: 0.7824 (mt) REVERT: B 981 PHE cc_start: 0.7892 (m-10) cc_final: 0.7636 (m-80) REVERT: C 931 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7977 (mp) REVERT: C 957 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7980 (mm-40) REVERT: C 963 VAL cc_start: 0.9059 (t) cc_final: 0.8835 (m) REVERT: C 983 ARG cc_start: 0.7577 (mtp180) cc_final: 0.7366 (ttp-170) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.6140 time to fit residues: 32.8951 Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2577 Z= 0.165 Angle : 0.377 7.415 3477 Z= 0.200 Chirality : 0.036 0.145 432 Planarity : 0.001 0.009 456 Dihedral : 2.993 15.003 339 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.02 % Allowed : 15.82 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.96 (0.44), residues: 327 helix: 4.95 (0.26), residues: 252 sheet: None (None), residues: 0 loop : -0.12 (0.77), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 954 PHE 0.008 0.001 PHE B 981 ARG 0.002 0.001 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 55 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7954 (m-10) cc_final: 0.7683 (m-80) REVERT: B 977 LEU cc_start: 0.8356 (mt) cc_final: 0.7779 (mt) REVERT: B 981 PHE cc_start: 0.7851 (m-10) cc_final: 0.7607 (m-80) REVERT: C 957 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7956 (mm-40) REVERT: C 963 VAL cc_start: 0.9045 (t) cc_final: 0.8826 (m) REVERT: C 983 ARG cc_start: 0.7576 (mtp180) cc_final: 0.7360 (ttp-170) outliers start: 6 outliers final: 2 residues processed: 51 average time/residue: 0.6222 time to fit residues: 33.2702 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN F1159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2577 Z= 0.226 Angle : 0.384 4.954 3477 Z= 0.212 Chirality : 0.038 0.147 432 Planarity : 0.002 0.010 456 Dihedral : 3.135 15.634 339 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.35 % Allowed : 16.16 % Favored : 82.49 % 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: 5.83 (0.44), residues: 327 helix: 4.85 (0.26), residues: 252 sheet: None (None), residues: 0 loop : -0.13 (0.77), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.009 0.001 PHE B 981 ARG 0.002 0.001 ARG B 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 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7956 (m-10) cc_final: 0.7668 (m-80) REVERT: B 977 LEU cc_start: 0.8374 (mt) cc_final: 0.7794 (mt) REVERT: B 981 PHE cc_start: 0.7857 (m-10) cc_final: 0.7616 (m-80) REVERT: C 957 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7987 (mm-40) REVERT: C 963 VAL cc_start: 0.9061 (t) cc_final: 0.8835 (m) REVERT: C 983 ARG cc_start: 0.7572 (mtp180) cc_final: 0.7360 (ttp-170) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.7112 time to fit residues: 38.0438 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.0470 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN C 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2577 Z= 0.174 Angle : 0.392 7.863 3477 Z= 0.208 Chirality : 0.037 0.148 432 Planarity : 0.001 0.010 456 Dihedral : 3.065 15.839 339 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 17.51 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.04 (0.44), residues: 327 helix: 5.00 (0.26), residues: 252 sheet: None (None), residues: 0 loop : -0.04 (0.77), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F1159 PHE 0.009 0.001 PHE B 981 ARG 0.002 0.001 ARG B 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 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 981 PHE cc_start: 0.7958 (m-10) cc_final: 0.7658 (m-80) REVERT: B 977 LEU cc_start: 0.8328 (mt) cc_final: 0.7751 (mt) REVERT: B 981 PHE cc_start: 0.7828 (m-10) cc_final: 0.7569 (m-80) REVERT: C 957 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7963 (mm-40) REVERT: C 963 VAL cc_start: 0.9043 (t) cc_final: 0.8827 (m) REVERT: C 983 ARG cc_start: 0.7581 (mtp180) cc_final: 0.7324 (ttp-170) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.6337 time to fit residues: 33.1998 Evaluate side-chains 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain E residue 1176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.143371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.121579 restraints weight = 3547.509| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.13 r_work: 0.3928 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2577 Z= 0.188 Angle : 0.372 5.382 3477 Z= 0.204 Chirality : 0.037 0.145 432 Planarity : 0.001 0.010 456 Dihedral : 3.082 15.766 339 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.01 % Allowed : 17.17 % 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: 6.00 (0.44), residues: 327 helix: 4.96 (0.26), residues: 252 sheet: None (None), residues: 0 loop : -0.01 (0.78), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.009 0.001 PHE B 981 ARG 0.002 0.001 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1279.17 seconds wall clock time: 23 minutes 30.74 seconds (1410.74 seconds total)