Starting phenix.real_space_refine on Thu Dec 7 15:50:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/12_2023/7c1d_30269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/12_2023/7c1d_30269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/12_2023/7c1d_30269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/12_2023/7c1d_30269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/12_2023/7c1d_30269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c1d_30269/12_2023/7c1d_30269.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 1254 2.51 5 N 360 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 2034 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.41, per 1000 atoms: 0.69 Number of scatterers: 2034 At special positions: 0 Unit cell: (105.768, 61.02, 33.9, 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 420 8.00 N 360 7.00 C 1254 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: 0.80 Conformation dependent library (CDL) restraints added in 416.3 milliseconds 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.602A pdb=" N ALA E 53 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.585A pdb=" N ALA F 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA C 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 0.02 Time building geometry restraints manager: 0.87 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: 372 1.29 - 1.36: 336 1.36 - 1.42: 54 1.42 - 1.48: 348 1.48 - 1.55: 930 Bond restraints: 2040 Sorted by residual: bond pdb=" CB VAL F 66 " pdb=" CG2 VAL F 66 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.06e-01 bond pdb=" CB VAL E 66 " pdb=" CG2 VAL E 66 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.06e-01 bond pdb=" CB VAL D 66 " pdb=" CG2 VAL D 66 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.96e-01 bond pdb=" CB VAL C 66 " pdb=" CG2 VAL C 66 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.93e-01 bond pdb=" CB VAL B 66 " pdb=" CG2 VAL B 66 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.83e-01 ... (remaining 2035 not shown) Histogram of bond angle deviations from ideal: 105.97 - 110.99: 806 110.99 - 116.02: 652 116.02 - 121.04: 601 121.04 - 126.07: 701 126.07 - 131.09: 6 Bond angle restraints: 2766 Sorted by residual: angle pdb=" N GLY F 51 " pdb=" CA GLY F 51 " pdb=" C GLY F 51 " ideal model delta sigma weight residual 110.18 115.29 -5.11 1.56e+00 4.11e-01 1.07e+01 angle pdb=" N GLY A 51 " pdb=" CA GLY A 51 " pdb=" C GLY A 51 " ideal model delta sigma weight residual 110.18 115.28 -5.10 1.56e+00 4.11e-01 1.07e+01 angle pdb=" N GLY D 51 " pdb=" CA GLY D 51 " pdb=" C GLY D 51 " ideal model delta sigma weight residual 110.18 115.24 -5.06 1.56e+00 4.11e-01 1.05e+01 angle pdb=" N GLY E 51 " pdb=" CA GLY E 51 " pdb=" C GLY E 51 " ideal model delta sigma weight residual 110.18 115.24 -5.06 1.56e+00 4.11e-01 1.05e+01 angle pdb=" N GLY B 51 " pdb=" CA GLY B 51 " pdb=" C GLY B 51 " ideal model delta sigma weight residual 110.18 115.22 -5.04 1.56e+00 4.11e-01 1.04e+01 ... (remaining 2761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 1074 16.53 - 33.05: 78 33.05 - 49.58: 18 49.58 - 66.11: 0 66.11 - 82.63: 6 Dihedral angle restraints: 1176 sinusoidal: 360 harmonic: 816 Sorted by residual: dihedral pdb=" CA ILE E 88 " pdb=" C ILE E 88 " pdb=" N ALA E 89 " pdb=" CA ALA E 89 " ideal model delta harmonic sigma weight residual 180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ILE A 88 " pdb=" C ILE A 88 " pdb=" N ALA A 89 " pdb=" CA ALA A 89 " ideal model delta harmonic sigma weight residual 180.00 -164.14 -15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ILE C 88 " pdb=" C ILE C 88 " pdb=" N ALA C 89 " pdb=" CA ALA C 89 " ideal model delta harmonic sigma weight residual -180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 1173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 160 0.026 - 0.053: 93 0.053 - 0.079: 55 0.079 - 0.106: 28 0.106 - 0.132: 30 Chirality restraints: 366 Sorted by residual: chirality pdb=" CA VAL E 95 " pdb=" N VAL E 95 " pdb=" C VAL E 95 " pdb=" CB VAL E 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL B 95 " pdb=" N VAL B 95 " pdb=" C VAL B 95 " pdb=" CB VAL B 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL D 95 " pdb=" N VAL D 95 " pdb=" C VAL D 95 " pdb=" CB VAL D 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 363 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " 0.008 2.00e-02 2.50e+03 6.91e-03 8.35e-01 pdb=" CG PHE D 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.009 2.00e-02 2.50e+03 6.85e-03 8.22e-01 pdb=" CG PHE C 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.008 2.00e-02 2.50e+03 6.81e-03 8.12e-01 pdb=" CG PHE B 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.001 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 852 2.87 - 3.38: 1890 3.38 - 3.89: 3196 3.89 - 4.39: 3053 4.39 - 4.90: 6398 Nonbonded interactions: 15389 Sorted by model distance: nonbonded pdb=" O GLY A 84 " pdb=" OG SER A 87 " model vdw 2.367 2.440 nonbonded pdb=" O GLY C 84 " pdb=" OG SER C 87 " model vdw 2.367 2.440 nonbonded pdb=" O GLY B 84 " pdb=" OG SER B 87 " model vdw 2.368 2.440 nonbonded pdb=" O GLY F 84 " pdb=" OG SER F 87 " model vdw 2.368 2.440 nonbonded pdb=" O GLY D 84 " pdb=" OG SER D 87 " model vdw 2.368 2.440 ... (remaining 15384 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' } 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 group one per residue 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: 0.520 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: 2.300 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.080 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.004 0.030 2040 Z= 0.178 Angle : 0.709 5.111 2766 Z= 0.456 Chirality : 0.054 0.132 366 Planarity : 0.003 0.008 354 Dihedral : 13.995 82.631 660 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.41 % Favored : 79.59 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % 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: -6.46 (0.32), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.92 (0.25), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.002 HIS F 50 PHE 0.016 0.004 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.230 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1272 time to fit residues: 11.2430 Evaluate side-chains 51 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.239 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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: 0.7206 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2040 Z= 0.216 Angle : 0.653 4.057 2766 Z= 0.380 Chirality : 0.055 0.180 366 Planarity : 0.003 0.014 354 Dihedral : 5.343 18.990 300 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.83 % Favored : 75.17 % Rotamer: Outliers : 11.46 % Allowed : 10.94 % Favored : 77.60 % 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: -5.90 (0.37), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.49 (0.28), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.032 0.008 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 52 time to evaluate : 0.223 Fit side-chains outliers start: 22 outliers final: 20 residues processed: 60 average time/residue: 0.0674 time to fit residues: 5.3055 Evaluate side-chains 69 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0213 time to fit residues: 0.9948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.7154 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2040 Z= 0.188 Angle : 0.611 4.158 2766 Z= 0.354 Chirality : 0.055 0.219 366 Planarity : 0.003 0.013 354 Dihedral : 5.173 17.941 300 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.47 % Favored : 76.53 % Rotamer: Outliers : 2.60 % Allowed : 20.83 % Favored : 76.56 % 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: -5.56 (0.39), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.024 0.007 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.275 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.0736 time to fit residues: 5.1238 Evaluate side-chains 48 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.224 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0227 time to fit residues: 0.4044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2040 Z= 0.200 Angle : 0.613 4.313 2766 Z= 0.359 Chirality : 0.055 0.237 366 Planarity : 0.003 0.015 354 Dihedral : 5.305 19.381 300 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.19 % Favored : 73.81 % Rotamer: Outliers : 10.94 % Allowed : 17.19 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.41 (0.40), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.027 0.007 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.225 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 50 average time/residue: 0.0637 time to fit residues: 4.3810 Evaluate side-chains 58 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.226 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0236 time to fit residues: 0.9696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2040 Z= 0.191 Angle : 0.613 4.381 2766 Z= 0.356 Chirality : 0.055 0.238 366 Planarity : 0.003 0.016 354 Dihedral : 5.211 18.458 300 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.15 % Favored : 75.85 % Rotamer: Outliers : 1.56 % Allowed : 22.92 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.41), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 50 PHE 0.025 0.007 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.226 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.0652 time to fit residues: 3.9915 Evaluate side-chains 42 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.240 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0225 time to fit residues: 0.4017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN B 62 GLN ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2040 Z= 0.279 Angle : 0.727 6.049 2766 Z= 0.424 Chirality : 0.059 0.268 366 Planarity : 0.004 0.017 354 Dihedral : 5.905 22.263 300 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 6.77 % Allowed : 24.48 % Favored : 68.75 % 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: -5.40 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.036 0.010 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.222 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 48 average time/residue: 0.0621 time to fit residues: 4.0886 Evaluate side-chains 50 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.222 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0224 time to fit residues: 0.6611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2040 Z= 0.116 Angle : 0.565 6.186 2766 Z= 0.322 Chirality : 0.053 0.243 366 Planarity : 0.002 0.018 354 Dihedral : 4.555 16.468 300 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.31 % Favored : 84.69 % Rotamer: Outliers : 1.56 % Allowed : 27.08 % Favored : 71.35 % 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: -5.10 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.010 0.002 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.166 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.0424 time to fit residues: 2.8977 Evaluate side-chains 39 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.195 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0352 time to fit residues: 0.5598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0050 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2040 Z= 0.126 Angle : 0.562 5.000 2766 Z= 0.321 Chirality : 0.051 0.221 366 Planarity : 0.002 0.019 354 Dihedral : 4.565 17.795 300 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.43 % Favored : 78.57 % Rotamer: Outliers : 3.65 % Allowed : 31.77 % Favored : 64.58 % 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: -4.89 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.013 0.003 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.244 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 40 average time/residue: 0.0519 time to fit residues: 3.1983 Evaluate side-chains 39 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.210 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0234 time to fit residues: 0.5179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2040 Z= 0.168 Angle : 0.608 4.614 2766 Z= 0.349 Chirality : 0.054 0.210 366 Planarity : 0.003 0.020 354 Dihedral : 4.895 17.654 300 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.79 % Favored : 77.21 % Rotamer: Outliers : 2.08 % Allowed : 31.77 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.021 0.006 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.253 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 46 average time/residue: 0.0469 time to fit residues: 3.2236 Evaluate side-chains 44 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.211 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0230 time to fit residues: 0.4396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2040 Z= 0.205 Angle : 0.641 4.624 2766 Z= 0.371 Chirality : 0.054 0.158 366 Planarity : 0.003 0.020 354 Dihedral : 5.259 19.978 300 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.83 % Favored : 75.17 % Rotamer: Outliers : 1.04 % Allowed : 32.81 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 50 PHE 0.027 0.007 PHE A 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.227 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.0484 time to fit residues: 2.9138 Evaluate side-chains 38 residues out of total 204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.225 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0220 time to fit residues: 0.3591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 0.0060 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5461 r_free = 0.5461 target = 0.353477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5380 r_free = 0.5380 target = 0.266139 restraints weight = 2573.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5393 r_free = 0.5393 target = 0.260988 restraints weight = 5082.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5402 r_free = 0.5402 target = 0.258260 restraints weight = 5971.243| |-----------------------------------------------------------------------------| r_work (final): 0.5325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2040 Z= 0.106 Angle : 0.530 4.651 2766 Z= 0.302 Chirality : 0.049 0.146 366 Planarity : 0.002 0.020 354 Dihedral : 4.289 16.512 300 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 2.60 % Allowed : 33.33 % Favored : 64.06 % 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: -4.73 (0.42), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.010 0.002 PHE E 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 861.66 seconds wall clock time: 21 minutes 1.11 seconds (1261.11 seconds total)