Starting phenix.real_space_refine on Mon Sep 23 12:34:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/09_2024/8fa1_28947.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/09_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_28947/09_2024/8fa1_28947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/09_2024/8fa1_28947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/09_2024/8fa1_28947.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa1_28947/09_2024/8fa1_28947.cif" } 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. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2553 Number of models: 1 Model: "" Number of chains: 2 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: "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} Restraints were copied for chains: C, B, D, F Time building chain proxies: 1.95, per 1000 atoms: 0.76 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 - 3.00 Amino acid : True - 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: 0.66 Conformation dependent library (CDL) restraints added in 329.4 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: 3.776A 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: 0.68 Time building geometry restraints manager: 0.78 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: 0.00 - 1.35: 3351 1.35 - 2.70: 79 2.70 - 4.04: 14 4.04 - 5.39: 3 5.39 - 6.74: 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 3.120 nonbonded pdb=" ND2 ASN B 978 " pdb=" OD1 ASP E1163 " model vdw 2.333 3.120 nonbonded pdb=" ND2 ASN A 978 " pdb=" OD1 ASP D1163 " model vdw 2.388 3.120 nonbonded pdb=" NE2 GLN C 935 " pdb=" O ALA F1190 " model vdw 2.418 3.120 nonbonded pdb=" NE2 GLN A 935 " pdb=" O ALA D1190 " model vdw 2.429 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.830 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.130 Find NCS groups from input model: 0.080 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- 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 : 0.280 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: 0.4830 time to fit residues: 19.6565 Evaluate side-chains 37 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 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 E1159 HIS F1159 HIS F1173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2559 Z= 0.227 Angle : 0.466 7.260 3453 Z= 0.244 Chirality : 0.037 0.122 435 Planarity : 0.002 0.013 453 Dihedral : 3.347 11.744 339 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.03 % Allowed : 15.49 % 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: 3.49 (0.45), residues: 327 helix: 3.05 (0.29), residues: 252 sheet: None (None), residues: 0 loop : -0.41 (0.82), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E1159 PHE 0.006 0.001 PHE C 970 ARG 0.003 0.001 ARG A 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 48 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.281 Fit side-chains REVERT: B 980 ILE cc_start: 0.8913 (mt) cc_final: 0.8711 (mt) REVERT: C 973 ILE cc_start: 0.8998 (mt) cc_final: 0.8746 (mt) outliers start: 9 outliers final: 1 residues processed: 47 average time/residue: 0.4885 time to fit residues: 24.4028 Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.0070 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2559 Z= 0.168 Angle : 0.433 7.482 3453 Z= 0.222 Chirality : 0.036 0.130 435 Planarity : 0.002 0.012 453 Dihedral : 3.139 9.783 339 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 4.58 (0.46), residues: 327 helix: 3.85 (0.29), residues: 252 sheet: None (None), residues: 0 loop : -0.14 (0.84), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS F1159 PHE 0.004 0.001 PHE A 927 ARG 0.003 0.000 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 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.279 Fit side-chains REVERT: B 980 ILE cc_start: 0.8925 (mt) cc_final: 0.8715 (mt) REVERT: C 973 ILE cc_start: 0.9003 (mt) cc_final: 0.8757 (mt) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.4658 time to fit residues: 20.3927 Evaluate side-chains 39 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 973 ILE 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: 0.0770 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 26 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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: 0.7613 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2559 Z= 0.145 Angle : 0.413 7.649 3453 Z= 0.215 Chirality : 0.036 0.131 435 Planarity : 0.002 0.012 453 Dihedral : 3.005 9.901 339 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.69 % Allowed : 16.16 % 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: 5.02 (0.46), residues: 327 helix: 4.23 (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 0.004 0.001 PHE C 970 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: 8 poor density : 39 time to evaluate : 0.305 Fit side-chains REVERT: B 980 ILE cc_start: 0.8930 (mt) cc_final: 0.8642 (mt) REVERT: C 973 ILE cc_start: 0.9005 (mt) cc_final: 0.8757 (mt) outliers start: 8 outliers final: 2 residues processed: 44 average time/residue: 0.6108 time to fit residues: 28.2570 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER 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: 0.8980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.7618 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2559 Z= 0.164 Angle : 0.407 7.154 3453 Z= 0.215 Chirality : 0.036 0.130 435 Planarity : 0.002 0.011 453 Dihedral : 2.981 9.063 339 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.03 % Allowed : 14.48 % 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: 5.07 (0.46), residues: 327 helix: 4.26 (0.28), residues: 249 sheet: None (None), residues: 0 loop : 0.02 (0.83), 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 0.002 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 50 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.285 Fit side-chains REVERT: B 980 ILE cc_start: 0.8915 (mt) cc_final: 0.8698 (mt) REVERT: C 973 ILE cc_start: 0.9011 (mt) cc_final: 0.8761 (mt) outliers start: 9 outliers final: 3 residues processed: 47 average time/residue: 0.5692 time to fit residues: 28.1529 Evaluate side-chains 42 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2559 Z= 0.153 Angle : 0.416 7.148 3453 Z= 0.217 Chirality : 0.036 0.123 435 Planarity : 0.002 0.011 453 Dihedral : 2.964 9.123 339 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.69 % Allowed : 15.15 % 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: 5.22 (0.46), residues: 327 helix: 4.37 (0.28), residues: 249 sheet: None (None), residues: 0 loop : 0.06 (0.82), 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 0.003 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 46 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.256 Fit side-chains REVERT: B 980 ILE cc_start: 0.8926 (mt) cc_final: 0.8704 (mt) REVERT: C 973 ILE cc_start: 0.9008 (mt) cc_final: 0.8750 (mt) outliers start: 8 outliers final: 3 residues processed: 44 average time/residue: 0.5765 time to fit residues: 26.7103 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.0270 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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: 0.2141 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= 0.178 Angle : 0.426 7.509 3453 Z= 0.223 Chirality : 0.037 0.124 435 Planarity : 0.002 0.013 453 Dihedral : 3.013 9.961 339 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.69 % Allowed : 15.82 % 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: 5.17 (0.45), residues: 327 helix: 4.33 (0.28), residues: 249 sheet: None (None), residues: 0 loop : 0.02 (0.82), 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 0.003 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 47 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.308 Fit side-chains REVERT: B 980 ILE cc_start: 0.8945 (mt) cc_final: 0.8718 (mt) REVERT: C 973 ILE cc_start: 0.9001 (mt) cc_final: 0.8743 (mt) outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 0.6230 time to fit residues: 30.0811 Evaluate side-chains 42 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 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** B 978 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2559 Z= 0.224 Angle : 0.445 7.392 3453 Z= 0.234 Chirality : 0.038 0.137 435 Planarity : 0.002 0.012 453 Dihedral : 3.142 11.164 339 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.36 % Allowed : 15.49 % 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: 4.99 (0.45), residues: 327 helix: 4.19 (0.28), residues: 249 sheet: None (None), residues: 0 loop : -0.01 (0.81), 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 0.003 0.000 ARG A 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 45 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.286 Fit side-chains REVERT: A 964 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8274 (ttmt) REVERT: B 980 ILE cc_start: 0.8932 (mt) cc_final: 0.8729 (mt) REVERT: C 973 ILE cc_start: 0.8973 (mt) cc_final: 0.8714 (mt) outliers start: 7 outliers final: 2 residues processed: 43 average time/residue: 0.5974 time to fit residues: 27.0901 Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain E 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: 0.8980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 21 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 2 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2559 Z= 0.134 Angle : 0.426 7.962 3453 Z= 0.223 Chirality : 0.037 0.166 435 Planarity : 0.002 0.015 453 Dihedral : 3.015 12.037 339 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: 5.36 (0.45), residues: 327 helix: 4.48 (0.28), residues: 249 sheet: None (None), residues: 0 loop : 0.07 (0.81), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F1159 PHE 0.004 0.001 PHE A 927 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 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.284 Fit side-chains REVERT: C 973 ILE cc_start: 0.8977 (mt) cc_final: 0.8720 (mt) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.5703 time to fit residues: 24.6893 Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** F1159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2559 Z= 0.193 Angle : 0.455 8.245 3453 Z= 0.236 Chirality : 0.038 0.153 435 Planarity : 0.002 0.017 453 Dihedral : 3.110 12.361 339 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.02 % Allowed : 16.84 % 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: 5.11 (0.45), residues: 327 helix: 4.28 (0.28), residues: 249 sheet: None (None), residues: 0 loop : 0.02 (0.81), 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 0.003 0.001 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 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.261 Fit side-chains REVERT: C 973 ILE cc_start: 0.8978 (mt) cc_final: 0.8719 (mt) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.5843 time to fit residues: 25.9804 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 4 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: ** 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 = 0.4378 r_free = 0.4378 target = 0.142122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.124151 restraints weight = 3534.351| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.19 r_work: 0.3913 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2559 Z= 0.213 Angle : 0.467 8.311 3453 Z= 0.247 Chirality : 0.038 0.149 435 Planarity : 0.002 0.018 453 Dihedral : 3.164 12.401 339 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.68 % Allowed : 16.84 % 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: 4.97 (0.45), residues: 327 helix: 4.19 (0.27), residues: 249 sheet: None (None), residues: 0 loop : -0.04 (0.80), 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 0.003 0.001 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1182.03 seconds wall clock time: 21 minutes 20.83 seconds (1280.83 seconds total)