Starting phenix.real_space_refine on Sun Mar 10 14:16:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8awt_15696/03_2024/8awt_15696_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8awt_15696/03_2024/8awt_15696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8awt_15696/03_2024/8awt_15696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8awt_15696/03_2024/8awt_15696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8awt_15696/03_2024/8awt_15696_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8awt_15696/03_2024/8awt_15696_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.002 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 1190 2.51 5 N 340 2.21 5 O 380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "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: 1910 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Chain: "B" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Chain: "C" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Chain: "D" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Chain: "E" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Chain: "F" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Chain: "G" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Chain: "H" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Chain: "I" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Chain: "J" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 191 Unusual residues: {'NH2': 1} Classifications: {'peptide': 26, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 25} Time building chain proxies: 1.28, per 1000 atoms: 0.67 Number of scatterers: 1910 At special positions: 0 Unit cell: (67.5, 58.5, 43.2, 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 380 8.00 N 340 7.00 C 1190 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: 0.81 Conformation dependent library (CDL) restraints added in 347.8 milliseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.84 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: 310 1.29 - 1.35: 330 1.35 - 1.41: 220 1.41 - 1.48: 320 1.48 - 1.54: 760 Bond restraints: 1940 Sorted by residual: bond pdb=" CA VAL H 32 " pdb=" CB VAL H 32 " ideal model delta sigma weight residual 1.542 1.536 0.006 1.26e-02 6.30e+03 1.95e-01 bond pdb=" CA PHE A 15 " pdb=" CB PHE A 15 " ideal model delta sigma weight residual 1.535 1.527 0.008 2.02e-02 2.45e+03 1.64e-01 bond pdb=" CA PHE E 15 " pdb=" CB PHE E 15 " ideal model delta sigma weight residual 1.535 1.527 0.008 2.02e-02 2.45e+03 1.62e-01 bond pdb=" CA VAL B 32 " pdb=" CB VAL B 32 " ideal model delta sigma weight residual 1.542 1.537 0.005 1.26e-02 6.30e+03 1.61e-01 bond pdb=" CA VAL J 32 " pdb=" CB VAL J 32 " ideal model delta sigma weight residual 1.542 1.537 0.005 1.26e-02 6.30e+03 1.59e-01 ... (remaining 1935 not shown) Histogram of bond angle deviations from ideal: 106.09 - 111.13: 837 111.13 - 116.17: 384 116.17 - 121.21: 833 121.21 - 126.25: 576 126.25 - 131.28: 10 Bond angle restraints: 2640 Sorted by residual: angle pdb=" C PHE D 23 " pdb=" N GLY D 24 " pdb=" CA GLY D 24 " ideal model delta sigma weight residual 122.38 120.63 1.75 1.08e+00 8.57e-01 2.62e+00 angle pdb=" C PHE F 23 " pdb=" N GLY F 24 " pdb=" CA GLY F 24 " ideal model delta sigma weight residual 122.38 120.67 1.71 1.08e+00 8.57e-01 2.52e+00 angle pdb=" C PHE C 23 " pdb=" N GLY C 24 " pdb=" CA GLY C 24 " ideal model delta sigma weight residual 122.38 120.67 1.71 1.08e+00 8.57e-01 2.50e+00 angle pdb=" C PHE G 23 " pdb=" N GLY G 24 " pdb=" CA GLY G 24 " ideal model delta sigma weight residual 122.38 120.67 1.71 1.08e+00 8.57e-01 2.50e+00 angle pdb=" C PHE I 23 " pdb=" N GLY I 24 " pdb=" CA GLY I 24 " ideal model delta sigma weight residual 122.38 120.68 1.70 1.08e+00 8.57e-01 2.46e+00 ... (remaining 2635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.25: 930 8.25 - 16.50: 95 16.50 - 24.74: 15 24.74 - 32.99: 10 32.99 - 41.24: 10 Dihedral angle restraints: 1060 sinusoidal: 340 harmonic: 720 Sorted by residual: dihedral pdb=" N PHE B 15 " pdb=" CA PHE B 15 " pdb=" CB PHE B 15 " pdb=" CG PHE B 15 " ideal model delta sinusoidal sigma weight residual -180.00 -147.71 -32.29 3 1.50e+01 4.44e-03 5.31e+00 dihedral pdb=" N PHE D 15 " pdb=" CA PHE D 15 " pdb=" CB PHE D 15 " pdb=" CG PHE D 15 " ideal model delta sinusoidal sigma weight residual -180.00 -147.71 -32.29 3 1.50e+01 4.44e-03 5.31e+00 dihedral pdb=" N PHE J 15 " pdb=" CA PHE J 15 " pdb=" CB PHE J 15 " pdb=" CG PHE J 15 " ideal model delta sinusoidal sigma weight residual 180.00 -147.72 -32.28 3 1.50e+01 4.44e-03 5.30e+00 ... (remaining 1057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 176 0.024 - 0.047: 98 0.047 - 0.071: 6 0.071 - 0.094: 0 0.094 - 0.118: 30 Chirality restraints: 310 Sorted by residual: chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE C 26 " pdb=" N ILE C 26 " pdb=" C ILE C 26 " pdb=" CB ILE C 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 chirality pdb=" CA ILE I 26 " pdb=" N ILE I 26 " pdb=" C ILE I 26 " pdb=" CB ILE I 26 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 307 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 23 " 0.004 2.00e-02 2.50e+03 3.11e-03 1.69e-01 pdb=" CG PHE I 23 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE I 23 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE I 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE I 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 23 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE I 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 23 " 0.004 2.00e-02 2.50e+03 3.10e-03 1.68e-01 pdb=" CG PHE D 23 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE D 23 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 23 " 0.004 2.00e-02 2.50e+03 3.09e-03 1.67e-01 pdb=" CG PHE F 23 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 23 " 0.002 2.00e-02 2.50e+03 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.67 - 3.12: 1405 3.12 - 3.56: 1746 3.56 - 4.01: 2722 4.01 - 4.45: 3624 4.45 - 4.90: 5711 Nonbonded interactions: 15208 Sorted by model distance: nonbonded pdb=" N ALA E 13 " pdb=" O ALA E 13 " model vdw 2.671 2.496 nonbonded pdb=" N ALA A 13 " pdb=" O ALA A 13 " model vdw 2.671 2.496 nonbonded pdb=" N ALA I 13 " pdb=" O ALA I 13 " model vdw 2.672 2.496 nonbonded pdb=" N ALA G 13 " pdb=" O ALA G 13 " model vdw 2.672 2.496 nonbonded pdb=" N ALA C 13 " pdb=" O ALA C 13 " model vdw 2.672 2.496 ... (remaining 15203 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.150 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: 5.300 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.190 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.003 0.011 1940 Z= 0.152 Angle : 0.469 3.013 2640 Z= 0.275 Chirality : 0.040 0.118 310 Planarity : 0.001 0.003 350 Dihedral : 9.301 41.237 600 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.21), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.16), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 18 PHE 0.007 0.002 PHE H 23 TYR 0.001 0.000 TYR F 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.202 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1912 time to fit residues: 5.8904 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 35 ASN B 21 ASN C 21 ASN D 21 ASN E 35 ASN F 21 ASN H 21 ASN I 21 ASN J 21 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 1940 Z= 0.181 Angle : 0.489 6.000 2640 Z= 0.247 Chirality : 0.042 0.112 310 Planarity : 0.002 0.008 350 Dihedral : 4.184 11.054 260 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.22), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.17), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 18 PHE 0.012 0.002 PHE J 23 TYR 0.002 0.000 TYR C 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2438 time to fit residues: 1.1138 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 overall best weight: 2.4162 ------------------------------------------------------------------------------- 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: 0.8321 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 1940 Z= 0.193 Angle : 0.467 4.708 2640 Z= 0.241 Chirality : 0.042 0.112 310 Planarity : 0.002 0.005 350 Dihedral : 4.203 11.095 260 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.23), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.17), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 18 PHE 0.011 0.002 PHE J 23 TYR 0.002 0.000 TYR C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2382 time to fit residues: 0.8217 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 0.0070 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- 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: 0.8278 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.006 1940 Z= 0.072 Angle : 0.384 4.052 2640 Z= 0.196 Chirality : 0.041 0.112 310 Planarity : 0.001 0.004 350 Dihedral : 3.547 9.929 260 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: -3.62 (0.26), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.20), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.004 0.001 PHE J 23 TYR 0.001 0.000 TYR C 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.206 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.2253 time to fit residues: 2.0114 Evaluate side-chains 3 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS D 35 ASN E 18 HIS J 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.029 1940 Z= 0.334 Angle : 0.533 3.997 2640 Z= 0.286 Chirality : 0.044 0.112 310 Planarity : 0.003 0.007 350 Dihedral : 4.529 12.118 260 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.24), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.017 0.003 PHE J 23 TYR 0.003 0.001 TYR I 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2292 time to fit residues: 0.8213 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 0.0470 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- 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: 0.8355 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.023 1940 Z= 0.269 Angle : 0.500 3.860 2640 Z= 0.266 Chirality : 0.042 0.113 310 Planarity : 0.002 0.006 350 Dihedral : 4.431 11.839 260 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: -4.03 (0.26), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.20), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.014 0.003 PHE J 23 TYR 0.003 0.001 TYR C 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.2590 time to fit residues: 0.6314 Evaluate side-chains 1 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8309 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 1940 Z= 0.096 Angle : 0.396 3.080 2640 Z= 0.206 Chirality : 0.041 0.111 310 Planarity : 0.001 0.004 350 Dihedral : 3.737 10.376 260 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % 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: -3.69 (0.28), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.21), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 18 PHE 0.006 0.001 PHE G 23 TYR 0.001 0.000 TYR C 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.2398 time to fit residues: 1.1041 Evaluate side-chains 1 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1940 Z= 0.115 Angle : 0.404 3.083 2640 Z= 0.212 Chirality : 0.040 0.110 310 Planarity : 0.001 0.005 350 Dihedral : 3.814 10.637 260 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % 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: -3.53 (0.29), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.22), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 18 PHE 0.008 0.001 PHE J 23 TYR 0.001 0.000 TYR F 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2493 time to fit residues: 0.8343 Evaluate side-chains 1 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 1940 Z= 0.254 Angle : 0.480 3.629 2640 Z= 0.259 Chirality : 0.042 0.113 310 Planarity : 0.002 0.006 350 Dihedral : 4.392 12.266 260 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % 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: -3.83 (0.28), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.21), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 18 PHE 0.014 0.003 PHE J 23 TYR 0.003 0.001 TYR F 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.180 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.2140 time to fit residues: 0.7261 Evaluate side-chains 1 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 1940 Z= 0.314 Angle : 0.522 3.945 2640 Z= 0.284 Chirality : 0.043 0.114 310 Planarity : 0.003 0.007 350 Dihedral : 4.625 12.557 260 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % 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: -4.00 (0.28), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.21), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 18 PHE 0.016 0.003 PHE B 23 TYR 0.005 0.001 TYR F 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1 time to evaluate : 0.184 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.2383 time to fit residues: 0.5663 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061601 restraints weight = 2690.439| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.53 r_work: 0.2802 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 1940 Z= 0.205 Angle : 0.456 3.511 2640 Z= 0.244 Chirality : 0.041 0.112 310 Planarity : 0.002 0.006 350 Dihedral : 4.200 11.280 260 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % 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: -3.86 (0.30), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.23), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 18 PHE 0.013 0.002 PHE G 23 TYR 0.003 0.001 TYR C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 868.97 seconds wall clock time: 16 minutes 48.16 seconds (1008.16 seconds total)