Starting phenix.real_space_refine on Sun Mar 10 15:04:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/03_2024/8fa2_28948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/03_2024/8fa2_28948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/03_2024/8fa2_28948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/03_2024/8fa2_28948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/03_2024/8fa2_28948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/03_2024/8fa2_28948.pdb" } resolution = 2.82 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= 0.021 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 1590 2.51 5 N 453 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2577 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: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 323 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 323 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 323 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Time building chain proxies: 1.81, per 1000 atoms: 0.70 Number of scatterers: 2577 At special positions: 0 Unit cell: (48.975, 57.9538, 118.356, 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 453 7.00 C 1590 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: 1.13 Conformation dependent library (CDL) restraints added in 505.1 milliseconds 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 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: 12 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 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 1169 through 1173 Processing helix chain 'D' and resid 1180 through 1194 Processing helix chain 'D' and resid 1195 through 1197 No H-bonds generated for 'chain 'D' and resid 1195 through 1197' Processing helix chain 'E' and resid 1169 through 1173 Processing helix chain 'E' and resid 1180 through 1194 Processing helix chain 'E' and resid 1195 through 1197 No H-bonds generated for 'chain 'E' and resid 1195 through 1197' Processing helix chain 'F' and resid 1169 through 1173 Processing helix chain 'F' and resid 1180 through 1194 Processing helix chain 'F' and resid 1195 through 1197 No H-bonds generated for 'chain 'F' and resid 1195 through 1197' 238 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 483 1.29 - 1.35: 426 1.35 - 1.41: 71 1.41 - 1.48: 400 1.48 - 1.54: 1209 Bond restraints: 2589 Sorted by residual: bond pdb=" CA LEU A 966 " pdb=" C LEU A 966 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.29e-02 6.01e+03 1.01e+00 bond pdb=" CA LEU B 966 " pdb=" C LEU B 966 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.29e-02 6.01e+03 9.67e-01 bond pdb=" CA ILE A 980 " pdb=" C ILE A 980 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.18e-02 7.18e+03 8.96e-01 bond pdb=" N PHE B 970 " pdb=" CA PHE B 970 " ideal model delta sigma weight residual 1.459 1.448 0.012 1.23e-02 6.61e+03 8.75e-01 bond pdb=" CA ILE C 980 " pdb=" C ILE C 980 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.18e-02 7.18e+03 8.69e-01 ... (remaining 2584 not shown) Histogram of bond angle deviations from ideal: 103.18 - 108.78: 63 108.78 - 114.39: 1617 114.39 - 119.99: 743 119.99 - 125.59: 1060 125.59 - 131.19: 9 Bond angle restraints: 3492 Sorted by residual: angle pdb=" N ILE F1170 " pdb=" CA ILE F1170 " pdb=" C ILE F1170 " ideal model delta sigma weight residual 109.34 113.14 -3.80 2.08e+00 2.31e-01 3.33e+00 angle pdb=" N ILE E1170 " pdb=" CA ILE E1170 " pdb=" C ILE E1170 " ideal model delta sigma weight residual 109.34 113.13 -3.79 2.08e+00 2.31e-01 3.32e+00 angle pdb=" N ILE D1170 " pdb=" CA ILE D1170 " pdb=" C ILE D1170 " ideal model delta sigma weight residual 109.34 113.12 -3.78 2.08e+00 2.31e-01 3.31e+00 angle pdb=" CA LEU C 962 " pdb=" CB LEU C 962 " pdb=" CG LEU C 962 " ideal model delta sigma weight residual 116.30 122.21 -5.91 3.50e+00 8.16e-02 2.86e+00 angle pdb=" CA LEU B 962 " pdb=" CB LEU B 962 " pdb=" CG LEU B 962 " ideal model delta sigma weight residual 116.30 122.20 -5.90 3.50e+00 8.16e-02 2.84e+00 ... (remaining 3487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 1455 15.00 - 29.99: 111 29.99 - 44.99: 24 44.99 - 59.98: 6 59.98 - 74.98: 9 Dihedral angle restraints: 1605 sinusoidal: 621 harmonic: 984 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 -60.00 -119.75 59.75 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 -60.00 -119.72 59.72 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 -60.00 -119.68 59.68 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 196 0.021 - 0.043: 123 0.043 - 0.064: 73 0.064 - 0.086: 24 0.086 - 0.107: 16 Chirality restraints: 432 Sorted by residual: chirality pdb=" CA ILE F1173 " pdb=" N ILE F1173 " pdb=" C ILE F1173 " pdb=" CB ILE F1173 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.87e-01 chirality pdb=" CA ILE D1173 " pdb=" N ILE D1173 " pdb=" C ILE D1173 " pdb=" CB ILE D1173 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.71e-01 chirality pdb=" CA ILE D1199 " pdb=" N ILE D1199 " pdb=" C ILE D1199 " pdb=" CB ILE D1199 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.70e-01 ... (remaining 429 not shown) Planarity restraints: 459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 926 " -0.005 2.00e-02 2.50e+03 9.12e-03 8.32e-01 pdb=" C GLN A 926 " 0.016 2.00e-02 2.50e+03 pdb=" O GLN A 926 " -0.006 2.00e-02 2.50e+03 pdb=" N PHE A 927 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 926 " 0.004 2.00e-02 2.50e+03 8.87e-03 7.86e-01 pdb=" C GLN C 926 " -0.015 2.00e-02 2.50e+03 pdb=" O GLN C 926 " 0.006 2.00e-02 2.50e+03 pdb=" N PHE C 927 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 926 " -0.004 2.00e-02 2.50e+03 8.83e-03 7.80e-01 pdb=" C GLN B 926 " 0.015 2.00e-02 2.50e+03 pdb=" O GLN B 926 " -0.006 2.00e-02 2.50e+03 pdb=" N PHE B 927 " -0.005 2.00e-02 2.50e+03 ... (remaining 456 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 726 2.82 - 3.34: 2718 3.34 - 3.86: 4380 3.86 - 4.38: 4822 4.38 - 4.90: 8131 Nonbonded interactions: 20777 Sorted by model distance: nonbonded pdb=" OD1 ASN D1174 " pdb=" N ALA D1175 " model vdw 2.297 2.520 nonbonded pdb=" OD1 ASN F1174 " pdb=" N ALA F1175 " model vdw 2.297 2.520 nonbonded pdb=" OD1 ASN E1174 " pdb=" N ALA E1175 " model vdw 2.297 2.520 nonbonded pdb=" NZ LYS C 969 " pdb=" O GLY E1168 " model vdw 2.497 2.520 nonbonded pdb=" NZ LYS A 969 " pdb=" O GLY F1168 " model vdw 2.497 2.520 ... (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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.390 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.550 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 0.029 2589 Z= 0.398 Angle : 0.546 5.914 3492 Z= 0.326 Chirality : 0.039 0.107 432 Planarity : 0.002 0.009 459 Dihedral : 13.542 74.977 957 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % 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: -0.12 (0.39), residues: 330 helix: 0.33 (0.26), residues: 270 sheet: None (None), residues: 0 loop : -1.52 (0.68), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F1159 PHE 0.006 0.001 PHE A 981 ARG 0.001 0.000 ARG D1186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 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: 0 poor density : 45 time to evaluate : 0.273 Fit side-chains REVERT: B 970 PHE cc_start: 0.8964 (m-10) cc_final: 0.8760 (m-10) REVERT: C 954 HIS cc_start: 0.8541 (t-170) cc_final: 0.8237 (t-170) REVERT: C 980 ILE cc_start: 0.9080 (mt) cc_final: 0.8863 (mt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3737 time to fit residues: 18.2027 Evaluate side-chains 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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: 0.0770 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2589 Z= 0.162 Angle : 0.361 8.050 3492 Z= 0.190 Chirality : 0.034 0.129 432 Planarity : 0.002 0.009 459 Dihedral : 3.355 10.224 342 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 11.11 % Favored : 87.88 % 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: 3.93 (0.43), residues: 330 helix: 3.09 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.17 (0.72), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.006 0.001 PHE C 981 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 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: 3 poor density : 40 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 970 PHE cc_start: 0.8875 (m-10) cc_final: 0.8640 (m-10) REVERT: C 954 HIS cc_start: 0.8459 (t-170) cc_final: 0.8178 (t-170) outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 0.4414 time to fit residues: 19.4600 Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2589 Z= 0.243 Angle : 0.385 6.941 3492 Z= 0.206 Chirality : 0.036 0.111 432 Planarity : 0.002 0.009 459 Dihedral : 3.369 9.310 342 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 11.11 % Favored : 87.54 % 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: 4.60 (0.44), residues: 330 helix: 3.47 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.84 (0.79), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 954 PHE 0.007 0.001 PHE A 970 ARG 0.001 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.290 Fit side-chains REVERT: B 970 PHE cc_start: 0.8883 (m-10) cc_final: 0.8658 (m-10) REVERT: C 954 HIS cc_start: 0.8497 (t-170) cc_final: 0.8223 (t-170) REVERT: C 962 LEU cc_start: 0.8937 (tt) cc_final: 0.8615 (tp) REVERT: C 973 ILE cc_start: 0.9063 (mt) cc_final: 0.8809 (mt) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.4598 time to fit residues: 19.6949 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.0020 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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: 0.7707 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2589 Z= 0.181 Angle : 0.358 6.330 3492 Z= 0.187 Chirality : 0.034 0.111 432 Planarity : 0.002 0.010 459 Dihedral : 3.215 8.739 342 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 11.78 % Favored : 87.21 % 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 (0.44), residues: 330 helix: 3.88 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.18 (0.83), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 954 PHE 0.005 0.001 PHE A 970 ARG 0.001 0.000 ARG D1186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.314 Fit side-chains REVERT: B 970 PHE cc_start: 0.8853 (m-10) cc_final: 0.8551 (m-10) REVERT: C 954 HIS cc_start: 0.8494 (t-170) cc_final: 0.8242 (t-170) REVERT: C 973 ILE cc_start: 0.9033 (mt) cc_final: 0.8778 (mt) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.4722 time to fit residues: 20.1990 Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 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: 0.5980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2589 Z= 0.201 Angle : 0.371 8.219 3492 Z= 0.193 Chirality : 0.035 0.111 432 Planarity : 0.001 0.008 459 Dihedral : 3.191 8.772 342 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 12.46 % Favored : 86.53 % 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: 330 helix: 3.94 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.39 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.007 0.001 PHE A 970 ARG 0.001 0.000 ARG D1186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 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: 3 poor density : 40 time to evaluate : 0.286 Fit side-chains REVERT: B 970 PHE cc_start: 0.8852 (m-10) cc_final: 0.8569 (m-10) REVERT: C 954 HIS cc_start: 0.8501 (t-170) cc_final: 0.8251 (t-170) REVERT: C 973 ILE cc_start: 0.9053 (mt) cc_final: 0.8787 (mt) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.4351 time to fit residues: 19.1956 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2589 Z= 0.159 Angle : 0.334 6.821 3492 Z= 0.177 Chirality : 0.033 0.111 432 Planarity : 0.001 0.008 459 Dihedral : 3.100 8.617 342 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 12.79 % Favored : 86.20 % 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: 5.66 (0.45), residues: 330 helix: 4.13 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.60 (0.89), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.004 0.001 PHE B 927 ARG 0.001 0.000 ARG D1186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.290 Fit side-chains REVERT: B 970 PHE cc_start: 0.8824 (m-10) cc_final: 0.8532 (m-10) REVERT: C 954 HIS cc_start: 0.8493 (t-170) cc_final: 0.8254 (t-170) REVERT: C 973 ILE cc_start: 0.9033 (mt) cc_final: 0.8771 (mt) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.4656 time to fit residues: 19.4307 Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 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: 0.5980 chunk 14 optimal weight: 0.0370 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2589 Z= 0.168 Angle : 0.360 7.854 3492 Z= 0.187 Chirality : 0.034 0.113 432 Planarity : 0.001 0.008 459 Dihedral : 3.070 8.563 342 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 13.13 % Favored : 85.86 % 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: 5.75 (0.45), residues: 330 helix: 4.19 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.64 (0.89), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.004 0.001 PHE A 927 ARG 0.001 0.000 ARG D1186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.299 Fit side-chains REVERT: B 970 PHE cc_start: 0.8821 (m-10) cc_final: 0.8527 (m-10) REVERT: C 954 HIS cc_start: 0.8497 (t-170) cc_final: 0.8235 (t-170) REVERT: C 973 ILE cc_start: 0.9035 (mt) cc_final: 0.8777 (mt) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.4937 time to fit residues: 21.0976 Evaluate side-chains 39 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 0.0770 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2589 Z= 0.188 Angle : 0.373 8.471 3492 Z= 0.192 Chirality : 0.034 0.114 432 Planarity : 0.001 0.008 459 Dihedral : 3.101 8.732 342 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 12.46 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.64 (0.44), residues: 330 helix: 4.12 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.60 (0.89), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.004 0.001 PHE A 927 ARG 0.001 0.000 ARG D1186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.285 Fit side-chains REVERT: B 970 PHE cc_start: 0.8831 (m-10) cc_final: 0.8536 (m-10) REVERT: C 954 HIS cc_start: 0.8500 (t-170) cc_final: 0.8245 (t-170) REVERT: C 973 ILE cc_start: 0.9055 (mt) cc_final: 0.8797 (mt) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.4949 time to fit residues: 21.6669 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 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: 0.5980 chunk 14 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2589 Z= 0.140 Angle : 0.347 7.137 3492 Z= 0.182 Chirality : 0.033 0.114 432 Planarity : 0.001 0.008 459 Dihedral : 3.014 8.349 342 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 13.13 % Favored : 85.86 % 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: 5.95 (0.44), residues: 330 helix: 4.34 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.62 (0.87), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.004 0.001 PHE B 970 ARG 0.001 0.000 ARG D1186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.268 Fit side-chains REVERT: B 970 PHE cc_start: 0.8800 (m-10) cc_final: 0.8499 (m-10) REVERT: C 954 HIS cc_start: 0.8487 (t-170) cc_final: 0.8233 (t-170) REVERT: C 973 ILE cc_start: 0.9021 (mt) cc_final: 0.8767 (mt) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.4855 time to fit residues: 20.3197 Evaluate side-chains 40 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 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: 0.5980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2589 Z= 0.185 Angle : 0.371 8.972 3492 Z= 0.193 Chirality : 0.034 0.115 432 Planarity : 0.001 0.008 459 Dihedral : 3.055 8.480 342 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 13.80 % Favored : 85.52 % 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: 5.77 (0.44), residues: 330 helix: 4.22 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.58 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.004 0.001 PHE A 927 ARG 0.001 0.000 ARG D1186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.276 Fit side-chains REVERT: B 970 PHE cc_start: 0.8827 (m-10) cc_final: 0.8551 (m-10) REVERT: C 954 HIS cc_start: 0.8514 (t-170) cc_final: 0.8266 (t-170) REVERT: C 973 ILE cc_start: 0.9050 (mt) cc_final: 0.8791 (mt) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.4590 time to fit residues: 19.6447 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain E residue 1178 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: 1.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.144558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.129112 restraints weight = 3943.316| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.52 r_work: 0.3886 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2589 Z= 0.206 Angle : 0.361 6.213 3492 Z= 0.196 Chirality : 0.035 0.116 432 Planarity : 0.001 0.008 459 Dihedral : 3.126 8.824 342 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 13.80 % Favored : 85.52 % 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: 330 helix: 4.07 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.58 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 954 PHE 0.004 0.001 PHE A 927 ARG 0.001 0.000 ARG D1186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1064.06 seconds wall clock time: 19 minutes 44.08 seconds (1184.08 seconds total)