Starting phenix.real_space_refine (version: dev) on Sun Dec 11 13:03:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/12_2022/6vhl_21207_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/12_2022/6vhl_21207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/12_2022/6vhl_21207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/12_2022/6vhl_21207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/12_2022/6vhl_21207_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/12_2022/6vhl_21207_neut.pdb" } resolution = 3.3 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= 0.001 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 "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 1190 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Time building chain proxies: 1.11, per 1000 atoms: 0.93 Number of scatterers: 1190 At special positions: 0 Unit cell: (146.64, 78, 28.08, 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 2 16.00 O 226 8.00 N 220 7.00 C 742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 167.1 milliseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 268 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: 0.20 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: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 393 1.34 - 1.46: 184 1.46 - 1.57: 627 1.57 - 1.69: 0 1.69 - 1.80: 2 Bond restraints: 1206 Sorted by residual: bond pdb=" N ARG F 379 " pdb=" CA ARG F 379 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.34e+00 bond pdb=" N ARG E 379 " pdb=" CA ARG E 379 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.27e+00 bond pdb=" N LYS F 370 " pdb=" CA LYS F 370 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.20e-02 6.94e+03 6.51e+00 bond pdb=" CE LYS E 370 " pdb=" NZ LYS E 370 " ideal model delta sigma weight residual 1.489 1.426 0.063 3.00e-02 1.11e+03 4.43e+00 bond pdb=" N LYS F 369 " pdb=" CA LYS F 369 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.27e-02 6.20e+03 4.03e+00 ... (remaining 1201 not shown) Histogram of bond angle deviations from ideal: 102.45 - 108.22: 79 108.22 - 113.99: 678 113.99 - 119.77: 297 119.77 - 125.54: 534 125.54 - 131.32: 20 Bond angle restraints: 1608 Sorted by residual: angle pdb=" N LYS E 369 " pdb=" CA LYS E 369 " pdb=" CB LYS E 369 " ideal model delta sigma weight residual 110.44 117.19 -6.75 1.43e+00 4.89e-01 2.23e+01 angle pdb=" N LYS F 369 " pdb=" CA LYS F 369 " pdb=" C LYS F 369 " ideal model delta sigma weight residual 110.50 105.97 4.53 1.41e+00 5.03e-01 1.03e+01 angle pdb=" CA GLY E 367 " pdb=" C GLY E 367 " pdb=" N ASN E 368 " ideal model delta sigma weight residual 116.69 110.25 6.44 2.04e+00 2.40e-01 9.96e+00 angle pdb=" C THR E 377 " pdb=" N PHE E 378 " pdb=" CA PHE E 378 " ideal model delta sigma weight residual 122.67 126.92 -4.25 1.47e+00 4.63e-01 8.37e+00 angle pdb=" C THR F 377 " pdb=" N PHE F 378 " pdb=" CA PHE F 378 " ideal model delta sigma weight residual 122.67 126.91 -4.24 1.47e+00 4.63e-01 8.33e+00 ... (remaining 1603 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 12.67: 592 12.67 - 25.32: 86 25.32 - 37.98: 27 37.98 - 50.64: 17 50.64 - 63.29: 6 Dihedral angle restraints: 728 sinusoidal: 304 harmonic: 424 Sorted by residual: dihedral pdb=" C GLU F 380 " pdb=" N GLU F 380 " pdb=" CA GLU F 380 " pdb=" CB GLU F 380 " ideal model delta harmonic sigma weight residual -122.60 -132.58 9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C GLU E 380 " pdb=" N GLU E 380 " pdb=" CA GLU E 380 " pdb=" CB GLU E 380 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N GLU F 380 " pdb=" C GLU F 380 " pdb=" CA GLU F 380 " pdb=" CB GLU F 380 " ideal model delta harmonic sigma weight residual 122.80 132.04 -9.24 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 725 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.084: 147 0.084 - 0.167: 26 0.167 - 0.249: 3 0.249 - 0.332: 0 0.332 - 0.415: 2 Chirality restraints: 178 Sorted by residual: chirality pdb=" CA GLU F 380 " pdb=" N GLU F 380 " pdb=" C GLU F 380 " pdb=" CB GLU F 380 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA GLU E 380 " pdb=" N GLU E 380 " pdb=" C GLU E 380 " pdb=" CB GLU E 380 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA PHE E 378 " pdb=" N PHE E 378 " pdb=" C PHE E 378 " pdb=" CB PHE E 378 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 175 not shown) Planarity restraints: 206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 367 " -0.024 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C GLY E 367 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY E 367 " -0.035 2.00e-02 2.50e+03 pdb=" N ASN E 368 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 367 " 0.016 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C GLY F 367 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY F 367 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN F 368 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 331 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO E 332 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 332 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 332 " -0.027 5.00e-02 4.00e+02 ... (remaining 203 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 7 2.41 - 3.03: 635 3.03 - 3.66: 1387 3.66 - 4.28: 1677 4.28 - 4.90: 2417 Nonbonded interactions: 6123 Sorted by model distance: nonbonded pdb=" NZ LYS E 317 " pdb=" O GLY E 402 " model vdw 1.791 2.520 nonbonded pdb=" NZ LYS F 317 " pdb=" O GLY F 402 " model vdw 1.807 2.520 nonbonded pdb=" CE LYS F 317 " pdb=" O GLY F 402 " model vdw 1.970 3.440 nonbonded pdb=" CE LYS E 317 " pdb=" O GLY E 402 " model vdw 1.974 3.440 nonbonded pdb=" OG SER F 320 " pdb=" OD1 ASN F 368 " model vdw 2.392 2.440 ... (remaining 6118 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 'E' selection = chain 'F' } 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 2 5.16 5 C 742 2.51 5 N 220 2.21 5 O 226 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.820 Check model and map are aligned: 0.020 Convert atoms to be neutral: 0.000 Process input model: 8.960 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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 0.063 1206 Z= 0.362 Angle : 1.031 7.962 1608 Z= 0.579 Chirality : 0.072 0.415 178 Planarity : 0.008 0.051 206 Dihedral : 15.846 63.293 460 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.67 % Favored : 85.33 % Rotamer Outliers : 4.48 % 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: -6.30 (0.40), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.79 (0.30), residues: 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.160 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.2451 time to fit residues: 11.9623 Evaluate side-chains 28 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.162 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1077 time to fit residues: 0.5642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7015 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.027 1206 Z= 0.218 Angle : 0.713 5.264 1608 Z= 0.364 Chirality : 0.050 0.124 178 Planarity : 0.006 0.041 206 Dihedral : 6.163 17.380 160 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer Outliers : 5.22 % 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: -5.17 (0.50), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.38), residues: 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.163 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.1873 time to fit residues: 8.4971 Evaluate side-chains 39 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.162 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0204 time to fit residues: 0.3932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 1206 Z= 0.166 Angle : 0.621 5.266 1608 Z= 0.313 Chirality : 0.046 0.113 178 Planarity : 0.005 0.039 206 Dihedral : 5.684 16.910 160 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer Outliers : 2.99 % 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: -4.45 (0.55), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.42), residues: 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.156 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.1595 time to fit residues: 7.3422 Evaluate side-chains 40 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.156 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0162 time to fit residues: 0.2866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 1206 Z= 0.108 Angle : 0.608 5.570 1608 Z= 0.294 Chirality : 0.045 0.116 178 Planarity : 0.004 0.033 206 Dihedral : 5.052 15.400 160 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 2.99 % 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: -4.03 (0.58), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.44), residues: 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.155 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.1738 time to fit residues: 7.1930 Evaluate side-chains 36 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.161 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0174 time to fit residues: 0.2739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.0010 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.7531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 1206 Z= 0.124 Angle : 0.584 4.579 1608 Z= 0.284 Chirality : 0.044 0.113 178 Planarity : 0.004 0.036 206 Dihedral : 5.076 15.747 160 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.58), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.44), residues: 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.163 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.2020 time to fit residues: 7.6363 Evaluate side-chains 36 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.165 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0189 time to fit residues: 0.2515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 1206 Z= 0.184 Angle : 0.646 5.284 1608 Z= 0.315 Chirality : 0.045 0.109 178 Planarity : 0.004 0.032 206 Dihedral : 5.394 15.740 160 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 1.49 % 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: -3.85 (0.59), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.45), residues: 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.159 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.2010 time to fit residues: 7.8037 Evaluate side-chains 36 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.144 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0175 time to fit residues: 0.2666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.8243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 1206 Z= 0.109 Angle : 0.577 5.623 1608 Z= 0.278 Chirality : 0.044 0.118 178 Planarity : 0.004 0.031 206 Dihedral : 4.824 15.292 160 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.60), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.46), residues: 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.161 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.1860 time to fit residues: 8.0471 Evaluate side-chains 38 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.158 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0186 time to fit residues: 0.2434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 0.0370 chunk 13 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.0030 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN F 327 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.8377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 1206 Z= 0.097 Angle : 0.578 6.244 1608 Z= 0.276 Chirality : 0.044 0.116 178 Planarity : 0.004 0.042 206 Dihedral : 4.425 14.065 160 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 1.49 % 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: -3.61 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.46), residues: 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.160 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.2052 time to fit residues: 7.9730 Evaluate side-chains 37 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.155 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0176 time to fit residues: 0.2684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.8668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 1206 Z= 0.120 Angle : 0.560 5.686 1608 Z= 0.268 Chirality : 0.043 0.111 178 Planarity : 0.004 0.040 206 Dihedral : 4.497 12.679 160 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.47), residues: 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.159 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1870 time to fit residues: 7.8934 Evaluate side-chains 38 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.156 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0148 time to fit residues: 0.2442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.8842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 1206 Z= 0.127 Angle : 0.641 7.291 1608 Z= 0.291 Chirality : 0.043 0.109 178 Planarity : 0.004 0.040 206 Dihedral : 4.327 12.337 160 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.46), residues: 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.167 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.1929 time to fit residues: 7.5328 Evaluate side-chains 37 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.163 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0144 time to fit residues: 0.2445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.155011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.145405 restraints weight = 2966.981| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 3.98 r_work: 0.4347 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.8949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 1206 Z= 0.095 Angle : 0.581 6.602 1608 Z= 0.262 Chirality : 0.043 0.115 178 Planarity : 0.004 0.039 206 Dihedral : 4.080 12.230 160 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.46), residues: 150 =============================================================================== Job complete usr+sys time: 856.10 seconds wall clock time: 15 minutes 54.06 seconds (954.06 seconds total)