Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:47:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/11_2022/7m62_23687_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/11_2022/7m62_23687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/11_2022/7m62_23687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/11_2022/7m62_23687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/11_2022/7m62_23687_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/11_2022/7m62_23687_updated.pdb" } resolution = 3.9 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 Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2380 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: 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: "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: 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: "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: 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: "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: 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: "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: 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} Time building chain proxies: 1.77, per 1000 atoms: 0.74 Number of scatterers: 2380 At special positions: 0 Unit cell: (68.575, 72.795, 41.145, 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 10 16.00 O 480 8.00 N 440 7.00 C 1450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 376.9 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 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: 0.14 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: 1.15 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: 380 1.31 - 1.44: 740 1.44 - 1.56: 1280 1.56 - 1.68: 0 1.68 - 1.81: 10 Bond restraints: 2410 Sorted by residual: bond pdb=" CB ASN G 22 " pdb=" CG ASN G 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN H 22 " pdb=" CG ASN H 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN J 22 " pdb=" CG ASN J 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN I 22 " pdb=" CG ASN I 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" CB ASN A 22 " pdb=" CG ASN A 22 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 1.01e+01 ... (remaining 2405 not shown) Histogram of bond angle deviations from ideal: 105.63 - 110.74: 754 110.74 - 115.85: 813 115.85 - 120.95: 902 120.95 - 126.06: 791 126.06 - 131.17: 20 Bond angle restraints: 3280 Sorted by residual: angle pdb=" N ASN F 22 " pdb=" CA ASN F 22 " pdb=" C ASN F 22 " ideal model delta sigma weight residual 109.80 114.78 -4.98 1.70e+00 3.46e-01 8.59e+00 angle pdb=" N ASN B 22 " pdb=" CA ASN B 22 " pdb=" C ASN B 22 " ideal model delta sigma weight residual 109.80 114.78 -4.98 1.70e+00 3.46e-01 8.58e+00 angle pdb=" N ASN J 22 " pdb=" CA ASN J 22 " pdb=" C ASN J 22 " ideal model delta sigma weight residual 109.80 114.77 -4.97 1.70e+00 3.46e-01 8.54e+00 angle pdb=" N ASN E 22 " pdb=" CA ASN E 22 " pdb=" C ASN E 22 " ideal model delta sigma weight residual 109.80 114.75 -4.95 1.70e+00 3.46e-01 8.49e+00 angle pdb=" N ASN D 22 " pdb=" CA ASN D 22 " pdb=" C ASN D 22 " ideal model delta sigma weight residual 109.80 114.75 -4.95 1.70e+00 3.46e-01 8.49e+00 ... (remaining 3275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.29: 1110 11.29 - 22.58: 160 22.58 - 33.87: 70 33.87 - 45.17: 30 45.17 - 56.46: 10 Dihedral angle restraints: 1380 sinusoidal: 460 harmonic: 920 Sorted by residual: dihedral pdb=" CA ASN I 21 " pdb=" C ASN I 21 " pdb=" N ASN I 22 " pdb=" CA ASN I 22 " 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 ASN G 21 " pdb=" C ASN G 21 " pdb=" N ASN G 22 " pdb=" CA ASN G 22 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASN A 21 " pdb=" C ASN A 21 " pdb=" N ASN A 22 " pdb=" CA ASN A 22 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 1377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 299 0.059 - 0.118: 71 0.118 - 0.177: 10 0.177 - 0.236: 10 0.236 - 0.295: 10 Chirality restraints: 400 Sorted by residual: chirality pdb=" CB ILE H 26 " pdb=" CA ILE H 26 " pdb=" CG1 ILE H 26 " pdb=" CG2 ILE H 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE C 26 " pdb=" CA ILE C 26 " pdb=" CG1 ILE C 26 " pdb=" CG2 ILE C 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB ILE D 26 " pdb=" CA ILE D 26 " pdb=" CG1 ILE D 26 " pdb=" CG2 ILE D 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 397 not shown) Planarity restraints: 430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 20 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C SER D 20 " 0.020 2.00e-02 2.50e+03 pdb=" O SER D 20 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN D 21 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 20 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C SER H 20 " 0.020 2.00e-02 2.50e+03 pdb=" O SER H 20 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN H 21 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 20 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C SER C 20 " -0.020 2.00e-02 2.50e+03 pdb=" O SER C 20 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN C 21 " 0.007 2.00e-02 2.50e+03 ... (remaining 427 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 788 2.84 - 3.35: 2458 3.35 - 3.87: 4304 3.87 - 4.38: 4606 4.38 - 4.90: 9088 Nonbonded interactions: 21244 Sorted by model distance: nonbonded pdb=" O ASN A 22 " pdb=" N NH2 D 38 " model vdw 2.321 3.120 nonbonded pdb=" N NH2 B 38 " pdb=" O ASN E 22 " model vdw 2.321 3.120 nonbonded pdb=" O ASN C 22 " pdb=" N NH2 H 38 " model vdw 2.321 3.120 nonbonded pdb=" N NH2 F 38 " pdb=" O ASN I 22 " model vdw 2.321 3.120 nonbonded pdb=" O ASN B 22 " pdb=" N NH2 C 38 " model vdw 2.325 3.120 ... (remaining 21239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1450 2.51 5 N 440 2.21 5 O 480 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: 0.100 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: 0.790 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.020 Process input model: 10.850 Find NCS groups from input model: 0.170 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.079 2410 Z= 0.323 Angle : 1.131 5.506 3280 Z= 0.652 Chirality : 0.073 0.295 400 Planarity : 0.003 0.011 430 Dihedral : 14.835 56.457 780 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 32.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % 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: -4.97 (0.31), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.24), residues: 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.240 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2579 time to fit residues: 11.4574 Evaluate side-chains 20 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3615 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 40.0000 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 50.0000 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 21 ASN C 21 ASN D 21 ASN E 21 ASN F 21 ASN G 21 ASN H 21 ASN I 21 ASN J 21 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 2410 Z= 0.204 Angle : 0.977 8.143 3280 Z= 0.538 Chirality : 0.056 0.185 400 Planarity : 0.004 0.020 430 Dihedral : 12.314 36.033 330 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer Outliers : 6.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.87 % 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: -4.50 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.28), residues: 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 20 time to evaluate : 0.289 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 36 average time/residue: 0.1178 time to fit residues: 5.3780 Evaluate side-chains 25 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 15 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0289 time to fit residues: 0.8457 ------------------------------------------------------------------------------- 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: 10.0000 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 40.0000 chunk 29 optimal weight: 20.0000 chunk 24 optimal weight: 50.0000 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 chunk 26 optimal weight: 40.0000 chunk 20 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 overall best weight: 11.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 2410 Z= 0.248 Angle : 1.026 7.901 3280 Z= 0.558 Chirality : 0.064 0.360 400 Planarity : 0.003 0.013 430 Dihedral : 12.447 38.671 330 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 32.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer Outliers : 11.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.94 % 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: -4.52 (0.38), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.29), residues: 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 18 time to evaluate : 0.299 Fit side-chains outliers start: 31 outliers final: 26 residues processed: 48 average time/residue: 0.1171 time to fit residues: 7.1405 Evaluate side-chains 42 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 16 time to evaluate : 0.299 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.0338 time to fit residues: 1.8293 ------------------------------------------------------------------------------- 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: 40.0000 chunk 13 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 40.0000 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 overall best weight: 11.3996 ------------------------------------------------------------------------------- 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: 0.6367 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 2410 Z= 0.237 Angle : 1.040 8.128 3280 Z= 0.563 Chirality : 0.067 0.438 400 Planarity : 0.004 0.021 430 Dihedral : 12.397 33.049 330 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 30.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.67 % Favored : 77.33 % Rotamer Outliers : 5.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.58 % 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: -4.44 (0.38), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.29), residues: 300 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 20 time to evaluate : 0.293 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 36 average time/residue: 0.0999 time to fit residues: 4.7194 Evaluate side-chains 28 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 18 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0267 time to fit residues: 0.7939 ------------------------------------------------------------------------------- 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: 8.9990 chunk 11 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.0570 chunk 7 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 overall best weight: 5.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 14 ASN H 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 2410 Z= 0.143 Angle : 0.955 7.209 3280 Z= 0.517 Chirality : 0.064 0.444 400 Planarity : 0.003 0.018 430 Dihedral : 11.910 32.354 330 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.67 % Favored : 79.33 % Rotamer Outliers : 4.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -4.46 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.28), residues: 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 22 time to evaluate : 0.300 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 32 average time/residue: 0.1208 time to fit residues: 4.8543 Evaluate side-chains 24 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.233 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0227 time to fit residues: 0.4321 ------------------------------------------------------------------------------- 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: 40.0000 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 40.0000 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 3 optimal weight: 50.0000 chunk 16 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 overall best weight: 16.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 2410 Z= 0.318 Angle : 1.125 9.740 3280 Z= 0.598 Chirality : 0.069 0.489 400 Planarity : 0.004 0.015 430 Dihedral : 12.329 34.765 330 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.33 % Favored : 74.67 % Rotamer Outliers : 6.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.94 % 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: -4.50 (0.38), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.29), residues: 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 23 time to evaluate : 0.299 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 40 average time/residue: 0.0628 time to fit residues: 3.6943 Evaluate side-chains 31 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 21 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0273 time to fit residues: 0.8136 ------------------------------------------------------------------------------- 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: 20.0000 chunk 24 optimal weight: 40.0000 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- 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: 0.6125 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 2410 Z= 0.108 Angle : 0.896 6.887 3280 Z= 0.484 Chirality : 0.052 0.246 400 Planarity : 0.003 0.010 430 Dihedral : 11.515 31.859 330 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -4.54 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.28), residues: 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.298 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.0585 time to fit residues: 2.6889 Evaluate side-chains 24 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0339 time to fit residues: 0.6224 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 8.9990 chunk 26 optimal weight: 40.0000 chunk 27 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 11 optimal weight: 40.0000 chunk 21 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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: 0.6225 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 2410 Z= 0.183 Angle : 0.984 7.370 3280 Z= 0.522 Chirality : 0.055 0.347 400 Planarity : 0.003 0.011 430 Dihedral : 11.520 33.667 330 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.33 % Favored : 75.67 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.97 % 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: -4.58 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.29), residues: 300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 18 time to evaluate : 0.270 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 27 average time/residue: 0.0580 time to fit residues: 2.4927 Evaluate side-chains 21 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0294 time to fit residues: 0.5048 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 0.0000 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 chunk 14 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- 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: 0.5966 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 2410 Z= 0.106 Angle : 0.877 7.486 3280 Z= 0.467 Chirality : 0.048 0.198 400 Planarity : 0.003 0.018 430 Dihedral : 10.841 29.977 330 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.33 % Favored : 83.67 % 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: -4.61 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.28), residues: 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.308 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0622 time to fit residues: 1.9428 Evaluate side-chains 16 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3252 ------------------------------------------------------------------------------- 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: 7.9990 chunk 21 optimal weight: 40.0000 chunk 3 optimal weight: 0.2980 chunk 6 optimal weight: 30.0000 chunk 23 optimal weight: 0.0060 chunk 9 optimal weight: 40.0000 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 30.0000 chunk 17 optimal weight: 40.0000 overall best weight: 1.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 ASN F 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 2410 Z= 0.098 Angle : 0.897 8.395 3280 Z= 0.467 Chirality : 0.048 0.204 400 Planarity : 0.003 0.019 430 Dihedral : 10.541 27.985 330 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % 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: -4.72 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.27), residues: 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.297 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0714 time to fit residues: 2.2076 Evaluate side-chains 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3635 ------------------------------------------------------------------------------- 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: 30.0000 chunk 16 optimal weight: 40.0000 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 60.0000 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 ASN F 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.140540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.125756 restraints weight = 10344.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.127853 restraints weight = 6233.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.129299 restraints weight = 4211.443| |-----------------------------------------------------------------------------| r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.6768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 2410 Z= 0.136 Angle : 0.961 8.473 3280 Z= 0.489 Chirality : 0.050 0.232 400 Planarity : 0.003 0.017 430 Dihedral : 10.708 29.949 330 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.67 % Favored : 77.33 % 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: -4.56 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.28), residues: 300 =============================================================================== Job complete usr+sys time: 812.33 seconds wall clock time: 16 minutes 25.36 seconds (985.36 seconds total)