Starting phenix.real_space_refine (version: dev) on Thu Feb 16 21:43:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/02_2023/7m62_23687_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/02_2023/7m62_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_23687/02_2023/7m62_23687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/02_2023/7m62_23687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/02_2023/7m62_23687_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m62_23687/02_2023/7m62_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 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-4877/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: 1.63, per 1000 atoms: 0.68 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: 1.52 Conformation dependent library (CDL) restraints added in 419.7 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: 0.09 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: 1.18 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: 0.130 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: 0.660 Check model and map are aligned: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.600 ------------------------------------------------------------------------------- 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 : 0.295 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2923 time to fit residues: 13.0030 Evaluate side-chains 20 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3516 ------------------------------------------------------------------------------- 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: 0.9990 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: 7.7990 ------------------------------------------------------------------------------- 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: 0.6288 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 2410 Z= 0.185 Angle : 0.950 8.001 3280 Z= 0.526 Chirality : 0.056 0.178 400 Planarity : 0.004 0.019 430 Dihedral : 12.163 35.324 330 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.33 % Favored : 80.67 % Rotamer Outliers : 5.19 % 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: -4.59 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (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 35 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 21 time to evaluate : 0.280 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 33 average time/residue: 0.1230 time to fit residues: 5.1428 Evaluate side-chains 26 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 16 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0281 time to fit residues: 0.8580 ------------------------------------------------------------------------------- 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: 9.9990 chunk 18 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 40.0000 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 9 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.6279 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 2410 Z= 0.171 Angle : 0.922 7.272 3280 Z= 0.508 Chirality : 0.054 0.303 400 Planarity : 0.003 0.011 430 Dihedral : 11.961 34.633 330 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.00 % Favored : 78.00 % Rotamer Outliers : 5.19 % 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: -4.47 (0.38), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (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 30 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 16 time to evaluate : 0.278 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 28 average time/residue: 0.1445 time to fit residues: 4.9946 Evaluate side-chains 22 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 14 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0260 time to fit residues: 0.6765 ------------------------------------------------------------------------------- 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: 50.0000 chunk 13 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 40.0000 chunk 28 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.0020 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 overall best weight: 6.1794 ------------------------------------------------------------------------------- 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: 0.6257 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 2410 Z= 0.153 Angle : 0.923 7.504 3280 Z= 0.505 Chirality : 0.054 0.306 400 Planarity : 0.003 0.022 430 Dihedral : 11.739 30.654 330 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.00 % Favored : 78.00 % Rotamer Outliers : 9.63 % 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: -4.64 (0.37), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.28), 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 44 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 18 time to evaluate : 0.291 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 44 average time/residue: 0.1112 time to fit residues: 6.1705 Evaluate side-chains 30 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.289 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0256 time to fit residues: 1.0328 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 40.0000 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 70.0000 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2410 Z= 0.114 Angle : 0.886 6.881 3280 Z= 0.484 Chirality : 0.054 0.359 400 Planarity : 0.003 0.018 430 Dihedral : 11.338 28.994 330 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.00 % Favored : 81.00 % Rotamer Outliers : 5.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.27), 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 30 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 16 time to evaluate : 0.304 Fit side-chains outliers start: 14 outliers final: 2 residues processed: 30 average time/residue: 0.1397 time to fit residues: 5.3001 Evaluate side-chains 12 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 10 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0285 time to fit residues: 0.4659 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 50.0000 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 40.0000 chunk 2 optimal weight: 30.0000 chunk 9 optimal weight: 50.0000 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 0.0870 chunk 3 optimal weight: 50.0000 chunk 16 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- 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: 0.6163 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 2410 Z= 0.135 Angle : 0.895 6.757 3280 Z= 0.485 Chirality : 0.052 0.299 400 Planarity : 0.003 0.017 430 Dihedral : 11.153 28.626 330 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.33 % Favored : 78.67 % Rotamer Outliers : 3.70 % 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: -4.69 (0.36), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.27), 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 22 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 12 time to evaluate : 0.272 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 22 average time/residue: 0.2136 time to fit residues: 5.6819 Evaluate side-chains 18 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 10 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0306 time to fit residues: 0.7871 ------------------------------------------------------------------------------- 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: 30.0000 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 40.0000 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 2410 Z= 0.121 Angle : 0.867 7.048 3280 Z= 0.472 Chirality : 0.048 0.178 400 Planarity : 0.003 0.013 430 Dihedral : 10.926 29.468 330 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer Outliers : 1.11 % 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: -4.71 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.27), 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 16 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 13 time to evaluate : 0.308 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 0.1230 time to fit residues: 2.7271 Evaluate side-chains 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0231 time to fit residues: 0.4100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0370 chunk 22 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 27 optimal weight: 0.4980 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 24 optimal weight: 50.0000 chunk 17 optimal weight: 6.9990 overall best weight: 2.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 2410 Z= 0.102 Angle : 0.840 6.697 3280 Z= 0.458 Chirality : 0.048 0.162 400 Planarity : 0.002 0.012 430 Dihedral : 10.642 28.702 330 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.33 % Favored : 79.67 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.26), 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 14 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 10 time to evaluate : 0.328 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 13 average time/residue: 0.0776 time to fit residues: 1.7810 Evaluate side-chains 10 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 8 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0319 time to fit residues: 0.4688 ------------------------------------------------------------------------------- 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: 30.0000 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN D 14 ASN H 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 2410 Z= 0.125 Angle : 0.880 7.161 3280 Z= 0.470 Chirality : 0.048 0.161 400 Planarity : 0.003 0.013 430 Dihedral : 10.644 30.164 330 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.33 % Favored : 77.67 % Rotamer Outliers : 0.74 % 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: -4.83 (0.34), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.26), 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 11 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 9 time to evaluate : 0.350 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 9 average time/residue: 0.0770 time to fit residues: 1.5106 Evaluate side-chains 9 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4165 ------------------------------------------------------------------------------- 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: 20.0000 chunk 21 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN D 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 2410 Z= 0.164 Angle : 0.915 7.443 3280 Z= 0.490 Chirality : 0.050 0.194 400 Planarity : 0.003 0.011 430 Dihedral : 10.890 29.983 330 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.33 % Favored : 77.67 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (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 18 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 14 time to evaluate : 0.259 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 18 average time/residue: 0.0619 time to fit residues: 1.8838 Evaluate side-chains 13 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0261 time to fit residues: 0.4540 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 19 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 overall best weight: 11.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 21 ASN F 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.130729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.117740 restraints weight = 10611.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.119741 restraints weight = 5927.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.121033 restraints weight = 3733.294| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.6798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 2410 Z= 0.242 Angle : 1.017 8.294 3280 Z= 0.547 Chirality : 0.056 0.251 400 Planarity : 0.004 0.025 430 Dihedral : 11.312 29.970 330 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 31.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.00 % Favored : 74.00 % Rotamer Outliers : 2.22 % 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: -4.94 (0.35), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.27), residues: 300 =============================================================================== Job complete usr+sys time: 781.15 seconds wall clock time: 15 minutes 0.95 seconds (900.95 seconds total)