Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/11_2022/7m65_23689_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/11_2022/7m65_23689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/11_2022/7m65_23689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/11_2022/7m65_23689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/11_2022/7m65_23689_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m65_23689/11_2022/7m65_23689_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2025 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "D" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "E" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "F" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "H" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "I" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 238 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 31} Chain: "J" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Time building chain proxies: 1.83, per 1000 atoms: 0.90 Number of scatterers: 2025 At special positions: 0 Unit cell: (62.245, 68.575, 45.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 415 8.00 N 370 7.00 C 1235 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: 0.93 Conformation dependent library (CDL) restraints added in 342.2 milliseconds 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 337 1.31 - 1.44: 618 1.44 - 1.56: 1090 1.56 - 1.68: 0 1.68 - 1.81: 5 Bond restraints: 2050 Sorted by residual: bond pdb=" CG ASN C 35 " pdb=" OD1 ASN C 35 " ideal model delta sigma weight residual 1.231 1.189 0.042 1.90e-02 2.77e+03 4.93e+00 bond pdb=" CG ASN E 35 " pdb=" OD1 ASN E 35 " ideal model delta sigma weight residual 1.231 1.189 0.042 1.90e-02 2.77e+03 4.78e+00 bond pdb=" CG ASN I 35 " pdb=" OD1 ASN I 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.74e+00 bond pdb=" CG ASN G 35 " pdb=" OD1 ASN G 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.59e+00 bond pdb=" CG ASN A 35 " pdb=" OD1 ASN A 35 " ideal model delta sigma weight residual 1.231 1.190 0.041 1.90e-02 2.77e+03 4.55e+00 ... (remaining 2045 not shown) Histogram of bond angle deviations from ideal: 103.62 - 109.16: 224 109.16 - 114.71: 1001 114.71 - 120.26: 590 120.26 - 125.81: 960 125.81 - 131.36: 10 Bond angle restraints: 2785 Sorted by residual: angle pdb=" N PHE F 15 " pdb=" CA PHE F 15 " pdb=" C PHE F 15 " ideal model delta sigma weight residual 112.41 119.39 -6.98 1.30e+00 5.92e-01 2.88e+01 angle pdb=" N PHE J 15 " pdb=" CA PHE J 15 " pdb=" C PHE J 15 " ideal model delta sigma weight residual 112.41 119.38 -6.97 1.30e+00 5.92e-01 2.87e+01 angle pdb=" N PHE B 15 " pdb=" CA PHE B 15 " pdb=" C PHE B 15 " ideal model delta sigma weight residual 112.41 119.37 -6.96 1.30e+00 5.92e-01 2.87e+01 angle pdb=" N PHE D 15 " pdb=" CA PHE D 15 " pdb=" C PHE D 15 " ideal model delta sigma weight residual 112.41 119.36 -6.95 1.30e+00 5.92e-01 2.86e+01 angle pdb=" N PHE H 15 " pdb=" CA PHE H 15 " pdb=" C PHE H 15 " ideal model delta sigma weight residual 112.41 119.34 -6.93 1.30e+00 5.92e-01 2.84e+01 ... (remaining 2780 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 8.26: 870 8.26 - 16.50: 195 16.50 - 24.75: 55 24.75 - 33.00: 35 33.00 - 41.24: 10 Dihedral angle restraints: 1165 sinusoidal: 385 harmonic: 780 Sorted by residual: dihedral pdb=" CA PHE H 15 " pdb=" C PHE H 15 " pdb=" N LEU H 16 " pdb=" CA LEU H 16 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA PHE J 15 " pdb=" C PHE J 15 " pdb=" N LEU J 16 " pdb=" CA LEU J 16 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE D 15 " pdb=" C PHE D 15 " pdb=" N LEU D 16 " pdb=" CA LEU D 16 " ideal model delta harmonic sigma weight residual 180.00 152.49 27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 1162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 312 0.132 - 0.264: 23 0.264 - 0.396: 0 0.396 - 0.528: 0 0.528 - 0.660: 5 Chirality restraints: 340 Sorted by residual: chirality pdb=" CB ILE B 26 " pdb=" CA ILE B 26 " pdb=" CG1 ILE B 26 " pdb=" CG2 ILE B 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CB ILE J 26 " pdb=" CA ILE J 26 " pdb=" CG1 ILE J 26 " pdb=" CG2 ILE J 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CB ILE F 26 " pdb=" CA ILE F 26 " pdb=" CG1 ILE F 26 " pdb=" CG2 ILE F 26 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 337 not shown) Planarity restraints: 365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.70e+00 pdb=" CG PHE E 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE E 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE E 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.69e+00 pdb=" CG PHE I 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE I 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE I 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE I 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE I 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 15 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 15 " -0.015 2.00e-02 2.50e+03 1.24e-02 2.68e+00 pdb=" CG PHE A 15 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 15 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 15 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 15 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 15 " -0.003 2.00e-02 2.50e+03 ... (remaining 362 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 936 2.89 - 3.40: 2352 3.40 - 3.90: 3194 3.90 - 4.40: 3732 4.40 - 4.90: 6916 Nonbonded interactions: 17130 Sorted by model distance: nonbonded pdb=" O LEU J 16 " pdb=" CD2 LEU J 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU D 16 " pdb=" CD2 LEU D 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU B 16 " pdb=" CD2 LEU B 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU F 16 " pdb=" CD2 LEU F 16 " model vdw 2.392 3.460 nonbonded pdb=" O LEU H 16 " pdb=" CD2 LEU H 16 " model vdw 2.393 3.460 ... (remaining 17125 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1235 2.51 5 N 370 2.21 5 O 415 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.220 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: 0.640 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.020 Process input model: 11.120 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 0.009 0.063 2050 Z= 0.391 Angle : 1.398 11.663 2785 Z= 0.743 Chirality : 0.102 0.660 340 Planarity : 0.004 0.012 365 Dihedral : 12.046 41.242 655 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 33.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Rotamer Outliers : 0.00 % 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: -6.09 (0.25), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.19), residues: 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1453 time to fit residues: 9.1408 Evaluate side-chains 30 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 2050 Z= 0.196 Angle : 0.847 11.667 2785 Z= 0.403 Chirality : 0.045 0.137 340 Planarity : 0.003 0.021 365 Dihedral : 7.734 23.871 275 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.39 % Favored : 79.61 % Rotamer Outliers : 0.00 % 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: -6.11 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.65 (0.21), residues: 255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0837 time to fit residues: 4.0426 Evaluate side-chains 22 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.225 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2050 Z= 0.148 Angle : 0.739 10.014 2785 Z= 0.360 Chirality : 0.042 0.142 340 Planarity : 0.003 0.015 365 Dihedral : 7.137 23.287 275 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.47 % Favored : 83.53 % Rotamer Outliers : 0.00 % 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: -6.07 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.22), residues: 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0874 time to fit residues: 3.9693 Evaluate side-chains 25 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 2050 Z= 0.156 Angle : 0.794 10.945 2785 Z= 0.366 Chirality : 0.044 0.140 340 Planarity : 0.003 0.015 365 Dihedral : 7.050 21.547 275 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.43 % Favored : 81.57 % Rotamer Outliers : 0.00 % 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: -6.07 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.21), residues: 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.257 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0665 time to fit residues: 3.0778 Evaluate side-chains 24 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 40.0000 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 30.0000 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 30.0000 chunk 5 optimal weight: 40.0000 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS I 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 2050 Z= 0.107 Angle : 0.723 10.520 2785 Z= 0.335 Chirality : 0.042 0.141 340 Planarity : 0.002 0.010 365 Dihedral : 6.269 20.936 275 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer Outliers : 0.00 % 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: -5.86 (0.29), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.46 (0.22), residues: 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.249 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0647 time to fit residues: 3.2556 Evaluate side-chains 24 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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: 0.7114 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2050 Z= 0.160 Angle : 0.750 10.300 2785 Z= 0.359 Chirality : 0.044 0.138 340 Planarity : 0.003 0.012 365 Dihedral : 6.717 20.010 275 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.86 % Favored : 83.14 % Rotamer Outliers : 0.00 % 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: -6.09 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.63 (0.21), residues: 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.251 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0661 time to fit residues: 2.8957 Evaluate side-chains 21 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 18 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 2050 Z= 0.167 Angle : 0.793 10.721 2785 Z= 0.370 Chirality : 0.044 0.140 340 Planarity : 0.003 0.013 365 Dihedral : 6.951 20.335 275 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % Rotamer Outliers : 0.00 % 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: -6.07 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.62 (0.21), residues: 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.244 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0645 time to fit residues: 3.0058 Evaluate side-chains 22 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.243 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.0970 chunk 22 optimal weight: 30.0000 chunk 23 optimal weight: 50.0000 chunk 13 optimal weight: 40.0000 chunk 9 optimal weight: 30.0000 chunk 17 optimal weight: 40.0000 chunk 6 optimal weight: 0.3980 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 overall best weight: 6.2986 ------------------------------------------------------------------------------- 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: 0.7086 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2050 Z= 0.142 Angle : 0.759 10.018 2785 Z= 0.353 Chirality : 0.044 0.145 340 Planarity : 0.003 0.011 365 Dihedral : 6.754 22.811 275 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.25 % Favored : 82.75 % Rotamer Outliers : 0.00 % 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: -6.01 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.57 (0.21), residues: 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.248 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0840 time to fit residues: 3.8492 Evaluate side-chains 22 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 0.0370 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 50.0000 chunk 12 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 8 optimal weight: 0.0870 overall best weight: 3.4040 ------------------------------------------------------------------------------- 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: 0.7001 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 2050 Z= 0.111 Angle : 0.759 11.560 2785 Z= 0.341 Chirality : 0.044 0.149 340 Planarity : 0.002 0.011 365 Dihedral : 6.155 19.967 275 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer Outliers : 0.00 % 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 (0.28), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.48 (0.21), residues: 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0655 time to fit residues: 3.0577 Evaluate side-chains 24 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 3 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 overall best weight: 10.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 2050 Z= 0.212 Angle : 0.813 11.011 2785 Z= 0.389 Chirality : 0.046 0.163 340 Planarity : 0.003 0.016 365 Dihedral : 7.155 20.855 275 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.04 % Favored : 81.96 % Rotamer Outliers : 0.00 % 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: -6.19 (0.26), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.71 (0.20), residues: 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 510 Ramachandran restraints generated. 255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.250 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0668 time to fit residues: 2.6763 Evaluate side-chains 22 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 40.0000 chunk 20 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 overall best weight: 11.9994 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.085677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.078802 restraints weight = 9646.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080369 restraints weight = 5072.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.081394 restraints weight = 3131.589| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 2050 Z= 0.228 Angle : 0.878 11.548 2785 Z= 0.421 Chirality : 0.048 0.167 340 Planarity : 0.003 0.014 365 Dihedral : 7.691 22.164 275 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.25 % Favored : 82.75 % Rotamer Outliers : 0.00 % 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: -6.33 (0.26), residues: 255 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.82 (0.20), residues: 255 =============================================================================== Job complete usr+sys time: 699.03 seconds wall clock time: 13 minutes 20.74 seconds (800.74 seconds total)