Starting phenix.real_space_refine on Thu Dec 7 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/12_2023/7v49_31704.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/12_2023/7v49_31704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/12_2023/7v49_31704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/12_2023/7v49_31704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/12_2023/7v49_31704.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v49_31704/12_2023/7v49_31704.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 765 2.51 5 N 210 2.21 5 O 246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "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: 1221 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 407 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "A" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 407 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 407 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Time building chain proxies: 1.13, per 1000 atoms: 0.93 Number of scatterers: 1221 At special positions: 0 Unit cell: (78.44, 65.72, 28.62, 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 246 8.00 N 210 7.00 C 765 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: 0.40 Conformation dependent library (CDL) restraints added in 239.3 milliseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.281A pdb=" N ILE C 88 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 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: 0.01 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 213 1.29 - 1.35: 192 1.35 - 1.42: 54 1.42 - 1.48: 207 1.48 - 1.54: 561 Bond restraints: 1227 Sorted by residual: bond pdb=" CB VAL A 82 " pdb=" CG1 VAL A 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB VAL B 82 " pdb=" CG1 VAL B 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.11e+00 bond pdb=" CB VAL C 82 " pdb=" CG1 VAL C 82 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB VAL C 37 " pdb=" CG1 VAL C 37 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.96e-01 bond pdb=" CB VAL B 37 " pdb=" CG1 VAL B 37 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.70e-01 ... (remaining 1222 not shown) Histogram of bond angle deviations from ideal: 106.16 - 111.18: 562 111.18 - 116.20: 315 116.20 - 121.22: 418 121.22 - 126.23: 367 126.23 - 131.25: 3 Bond angle restraints: 1665 Sorted by residual: angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " ideal model delta sigma weight residual 116.30 123.99 -7.69 3.50e+00 8.16e-02 4.83e+00 angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " ideal model delta sigma weight residual 116.30 123.98 -7.68 3.50e+00 8.16e-02 4.81e+00 angle pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " ideal model delta sigma weight residual 116.30 123.97 -7.67 3.50e+00 8.16e-02 4.80e+00 angle pdb=" N ILE B 88 " pdb=" CA ILE B 88 " pdb=" C ILE B 88 " ideal model delta sigma weight residual 106.61 110.32 -3.71 1.78e+00 3.16e-01 4.34e+00 angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 106.61 110.28 -3.67 1.78e+00 3.16e-01 4.25e+00 ... (remaining 1660 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.48: 557 9.48 - 18.94: 91 18.94 - 28.41: 36 28.41 - 37.88: 3 37.88 - 47.34: 15 Dihedral angle restraints: 702 sinusoidal: 222 harmonic: 480 Sorted by residual: dihedral pdb=" CA THR B 81 " pdb=" C THR B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR A 81 " pdb=" C THR A 81 " pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR C 81 " pdb=" C THR C 81 " pdb=" N VAL C 82 " pdb=" CA VAL C 82 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 68 0.028 - 0.055: 77 0.055 - 0.082: 43 0.082 - 0.109: 19 0.109 - 0.136: 15 Chirality restraints: 222 Sorted by residual: chirality pdb=" CA VAL C 40 " pdb=" N VAL C 40 " pdb=" C VAL C 40 " pdb=" CB VAL C 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL B 40 " pdb=" N VAL B 40 " pdb=" C VAL B 40 " pdb=" CB VAL B 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 40 " pdb=" N VAL A 40 " pdb=" C VAL A 40 " pdb=" CB VAL A 40 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 219 not shown) Planarity restraints: 207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " -0.005 2.00e-02 2.50e+03 9.63e-03 9.27e-01 pdb=" C VAL B 70 " 0.017 2.00e-02 2.50e+03 pdb=" O VAL B 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL B 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 70 " -0.005 2.00e-02 2.50e+03 9.44e-03 8.90e-01 pdb=" C VAL A 70 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL A 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL A 71 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 70 " -0.005 2.00e-02 2.50e+03 9.16e-03 8.39e-01 pdb=" C VAL C 70 " 0.016 2.00e-02 2.50e+03 pdb=" O VAL C 70 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL C 71 " -0.005 2.00e-02 2.50e+03 ... (remaining 204 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 356 2.80 - 3.33: 1111 3.33 - 3.85: 1702 3.85 - 4.38: 1838 4.38 - 4.90: 3934 Nonbonded interactions: 8941 Sorted by model distance: nonbonded pdb=" O SER A 42 " pdb=" OG SER A 42 " model vdw 2.279 2.440 nonbonded pdb=" O SER B 42 " pdb=" OG SER B 42 " model vdw 2.279 2.440 nonbonded pdb=" O SER C 42 " pdb=" OG SER C 42 " model vdw 2.280 2.440 nonbonded pdb=" O LYS B 80 " pdb=" OG1 THR B 81 " model vdw 2.498 2.440 nonbonded pdb=" O LYS C 80 " pdb=" OG1 THR C 81 " model vdw 2.499 2.440 ... (remaining 8936 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.390 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.370 Find NCS groups from input model: 0.060 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 1227 Z= 0.293 Angle : 1.014 7.691 1665 Z= 0.570 Chirality : 0.057 0.136 222 Planarity : 0.004 0.010 207 Dihedral : 13.695 47.342 402 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 39.66 % Favored : 60.34 % Rotamer: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % 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: -7.67 (0.34), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.84 (0.26), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.007 0.002 PHE A 94 TYR 0.014 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.137 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1061 time to fit residues: 2.9984 Evaluate side-chains 10 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.135 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.6905 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1227 Z= 0.124 Angle : 0.765 6.609 1665 Z= 0.412 Chirality : 0.058 0.125 222 Planarity : 0.003 0.013 207 Dihedral : 6.232 18.172 180 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.11 % Favored : 79.89 % Rotamer: Outliers : 3.25 % Allowed : 17.89 % Favored : 78.86 % 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: -6.87 (0.36), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.23 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.031 0.006 PHE C 94 TYR 0.006 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 16 time to evaluate : 0.112 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 20 average time/residue: 0.0717 time to fit residues: 1.7981 Evaluate side-chains 13 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.111 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0386 time to fit residues: 0.1968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.6931 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1227 Z= 0.145 Angle : 0.770 6.095 1665 Z= 0.422 Chirality : 0.057 0.127 222 Planarity : 0.003 0.015 207 Dihedral : 6.375 17.041 180 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.97 % Favored : 81.03 % Rotamer: Outliers : 3.25 % Allowed : 15.45 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.74 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.13 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.019 0.004 PHE C 94 TYR 0.010 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.134 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 17 average time/residue: 0.0601 time to fit residues: 1.4174 Evaluate side-chains 16 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 12 time to evaluate : 0.127 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0287 time to fit residues: 0.3304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.6975 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1227 Z= 0.178 Angle : 0.795 5.794 1665 Z= 0.439 Chirality : 0.057 0.120 222 Planarity : 0.003 0.011 207 Dihedral : 6.757 17.570 180 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.01 % Favored : 72.99 % Rotamer: Outliers : 1.63 % Allowed : 20.33 % Favored : 78.05 % 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: -6.70 (0.39), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.10 (0.30), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.015 0.003 PHE C 94 TYR 0.012 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.128 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0685 time to fit residues: 1.4082 Evaluate side-chains 14 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.131 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0163 time to fit residues: 0.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.0770 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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: 0.6910 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1227 Z= 0.140 Angle : 0.753 6.742 1665 Z= 0.414 Chirality : 0.056 0.132 222 Planarity : 0.003 0.015 207 Dihedral : 6.234 16.971 180 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.26 % Favored : 78.74 % Rotamer: Outliers : 1.63 % Allowed : 24.39 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.63 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.05 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.014 0.003 PHE C 94 TYR 0.009 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.134 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0638 time to fit residues: 1.3215 Evaluate side-chains 14 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.128 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0273 time to fit residues: 0.2450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 chunk 17 optimal weight: 0.0010 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.3164 ------------------------------------------------------------------------------- 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: 0.6687 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1227 Z= 0.099 Angle : 0.626 4.882 1665 Z= 0.341 Chirality : 0.054 0.137 222 Planarity : 0.002 0.014 207 Dihedral : 4.947 13.714 180 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 0.81 % Allowed : 22.76 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.48 (0.37), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.94 (0.28), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.013 0.003 PHE A 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.127 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.0448 time to fit residues: 1.0298 Evaluate side-chains 12 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.126 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0163 time to fit residues: 0.1956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.6910 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1227 Z= 0.164 Angle : 0.707 5.159 1665 Z= 0.393 Chirality : 0.054 0.129 222 Planarity : 0.003 0.012 207 Dihedral : 6.092 16.803 180 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.14 % Favored : 75.86 % Rotamer: Outliers : 2.44 % Allowed : 21.95 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.43 (0.39), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.89 (0.30), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.010 0.003 PHE A 94 TYR 0.013 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.128 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.0598 time to fit residues: 1.1223 Evaluate side-chains 12 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 9 time to evaluate : 0.129 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0240 time to fit residues: 0.2742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.6779 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1227 Z= 0.105 Angle : 0.655 5.499 1665 Z= 0.361 Chirality : 0.054 0.164 222 Planarity : 0.002 0.011 207 Dihedral : 5.390 15.273 180 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Rotamer: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.31 (0.38), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.80 (0.29), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.012 0.002 PHE A 94 TYR 0.007 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0409 time to fit residues: 0.6892 Evaluate side-chains 10 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.0870 chunk 2 optimal weight: 0.0980 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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: 0.6661 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1227 Z= 0.091 Angle : 0.598 5.505 1665 Z= 0.329 Chirality : 0.053 0.149 222 Planarity : 0.002 0.009 207 Dihedral : 4.543 13.445 180 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 0.00 % Allowed : 22.76 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.06 (0.40), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.61 (0.31), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.009 0.002 PHE A 94 TYR 0.004 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0332 time to fit residues: 0.7354 Evaluate side-chains 12 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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: 0.6691 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1227 Z= 0.094 Angle : 0.602 5.687 1665 Z= 0.334 Chirality : 0.052 0.158 222 Planarity : 0.002 0.008 207 Dihedral : 4.756 13.621 180 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Rotamer: Outliers : 0.00 % Allowed : 24.39 % Favored : 75.61 % 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: -5.88 (0.42), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.32), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.007 0.002 PHE A 94 TYR 0.006 0.002 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.128 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0447 time to fit residues: 0.8144 Evaluate side-chains 10 residues out of total 123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.115616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.095479 restraints weight = 1869.015| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.49 r_work: 0.3831 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1227 Z= 0.094 Angle : 0.579 5.565 1665 Z= 0.321 Chirality : 0.051 0.138 222 Planarity : 0.002 0.007 207 Dihedral : 4.772 13.338 180 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.44), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.34), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.007 0.002 PHE A 94 TYR 0.007 0.002 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 882.43 seconds wall clock time: 21 minutes 27.88 seconds (1287.88 seconds total)