Starting phenix.real_space_refine on Thu Dec 7 16:34:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/12_2023/8fa2_28948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/12_2023/8fa2_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_28948/12_2023/8fa2_28948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/12_2023/8fa2_28948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/12_2023/8fa2_28948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fa2_28948/12_2023/8fa2_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-1.21rc1-5172/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: 1.80, 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: 1.05 Conformation dependent library (CDL) restraints added in 468.2 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: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 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: 0.66 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.810 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:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- 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 : 0.304 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.3823 time to fit residues: 18.6470 Evaluate side-chains 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4116 ------------------------------------------------------------------------------- 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: 0.6980 chunk 13 optimal weight: 3.9990 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: 0.7980 chunk 29 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2589 Z= 0.208 Angle : 0.374 7.855 3492 Z= 0.201 Chirality : 0.034 0.124 432 Planarity : 0.002 0.010 459 Dihedral : 3.441 10.592 342 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 10.77 % 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: 3.66 (0.43), residues: 330 helix: 2.88 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.20 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 954 PHE 0.020 0.002 PHE B 970 ARG 0.001 0.000 ARG D1186 *********************** 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 45 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.264 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.4404 time to fit residues: 19.8615 Evaluate side-chains 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0776 time to fit residues: 0.7247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN C 954 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2589 Z= 0.232 Angle : 0.387 6.436 3492 Z= 0.207 Chirality : 0.035 0.112 432 Planarity : 0.002 0.009 459 Dihedral : 3.352 10.523 342 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 11.45 % 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: 4.61 (0.44), residues: 330 helix: 3.45 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 0.99 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 954 PHE 0.012 0.002 PHE B 970 ARG 0.001 0.000 ARG D1186 *********************** 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 45 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.291 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.6293 time to fit residues: 27.9975 Evaluate side-chains 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0691 time to fit residues: 0.5966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2589 Z= 0.192 Angle : 0.349 6.273 3492 Z= 0.191 Chirality : 0.034 0.111 432 Planarity : 0.002 0.010 459 Dihedral : 3.211 10.655 342 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 12.12 % 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: 5.12 (0.44), residues: 330 helix: 3.78 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.28 (0.84), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 954 PHE 0.007 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 45 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.311 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.5298 time to fit residues: 23.5797 Evaluate side-chains 42 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0717 time to fit residues: 0.5667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 C 954 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2589 Z= 0.225 Angle : 0.392 7.044 3492 Z= 0.208 Chirality : 0.034 0.113 432 Planarity : 0.002 0.007 459 Dihedral : 3.236 10.914 342 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 12.46 % 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: 5.15 (0.44), residues: 330 helix: 3.78 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.42 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 954 PHE 0.015 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 47 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.269 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.5210 time to fit residues: 24.3559 Evaluate side-chains 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.293 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0714 time to fit residues: 0.5910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.0050 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 954 HIS ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2589 Z= 0.184 Angle : 0.362 6.805 3492 Z= 0.203 Chirality : 0.034 0.112 432 Planarity : 0.001 0.008 459 Dihedral : 3.092 9.841 342 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 13.80 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.50 (0.45), residues: 330 helix: 4.02 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.55 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 954 PHE 0.017 0.002 PHE C 970 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 42 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.285 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.5096 time to fit residues: 21.6525 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0667 time to fit residues: 0.4466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN C 954 HIS ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2589 Z= 0.216 Angle : 0.388 7.398 3492 Z= 0.211 Chirality : 0.034 0.113 432 Planarity : 0.001 0.008 459 Dihedral : 3.156 9.973 342 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.68 % Allowed : 13.80 % Favored : 84.51 % 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: 5.35 (0.44), residues: 330 helix: 3.89 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.63 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 954 PHE 0.017 0.002 PHE C 970 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 45 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.295 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 43 average time/residue: 0.4791 time to fit residues: 21.9675 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.286 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 954 HIS ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2589 Z= 0.231 Angle : 0.384 7.166 3492 Z= 0.214 Chirality : 0.035 0.116 432 Planarity : 0.001 0.006 459 Dihedral : 3.155 9.800 342 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.35 % Allowed : 14.48 % Favored : 84.18 % 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: 5.31 (0.44), residues: 330 helix: 3.86 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.60 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 954 PHE 0.010 0.001 PHE B 970 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 44 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.300 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.5075 time to fit residues: 22.1682 Evaluate side-chains 42 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0842 time to fit residues: 0.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 954 HIS C 955 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2589 Z= 0.238 Angle : 0.413 7.850 3492 Z= 0.225 Chirality : 0.035 0.116 432 Planarity : 0.002 0.006 459 Dihedral : 3.200 9.653 342 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 14.81 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.18 (0.44), residues: 330 helix: 3.78 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.54 (0.84), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 954 PHE 0.009 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 43 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.291 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 0.5056 time to fit residues: 22.0825 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2589 Z= 0.213 Angle : 0.413 8.819 3492 Z= 0.223 Chirality : 0.035 0.128 432 Planarity : 0.001 0.007 459 Dihedral : 3.153 9.658 342 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 15.15 % Favored : 84.18 % 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: 5.31 (0.44), residues: 330 helix: 3.87 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.57 (0.84), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 954 PHE 0.009 0.001 PHE B 970 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 42 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.257 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.5114 time to fit residues: 22.3113 Evaluate side-chains 41 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.144653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.128901 restraints weight = 3924.614| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.55 r_work: 0.3881 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 2589 Z= 0.210 Angle : 0.398 7.215 3492 Z= 0.221 Chirality : 0.035 0.154 432 Planarity : 0.001 0.007 459 Dihedral : 3.155 10.194 342 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.34 % Allowed : 15.15 % Favored : 84.51 % 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: 5.30 (0.44), residues: 330 helix: 3.86 (0.29), residues: 270 sheet: None (None), residues: 0 loop : 1.61 (0.84), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 954 PHE 0.009 0.001 PHE B 970 ARG 0.001 0.000 ARG D1186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1088.03 seconds wall clock time: 20 minutes 12.13 seconds (1212.13 seconds total)