Starting phenix.real_space_refine on Thu Dec 7 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkz_14058/12_2023/7qkz_14058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkz_14058/12_2023/7qkz_14058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkz_14058/12_2023/7qkz_14058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkz_14058/12_2023/7qkz_14058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkz_14058/12_2023/7qkz_14058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkz_14058/12_2023/7qkz_14058.pdb" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 540 2.51 5 N 126 2.21 5 O 144 1.98 5 H 891 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 1701 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "F" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "G" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "H" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "I" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 189 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Time building chain proxies: 0.99, per 1000 atoms: 0.58 Number of scatterers: 1701 At special positions: 0 Unit cell: (58.464, 57.456, 29.232, 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) O 144 8.00 N 126 7.00 C 540 6.00 H 891 1.00 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: 1.10 Conformation dependent library (CDL) restraints added in 119.2 milliseconds 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 198 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.096A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.645A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 308 through 310 removed outlier: 6.053A pdb=" N ILE D 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.544A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 308 through 310 removed outlier: 6.115A pdb=" N ILE G 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.554A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) 9 hydrogen bonds defined for protein. 27 hydrogen bond angles 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: 0.40 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.08: 215 1.08 - 1.20: 676 1.20 - 1.33: 197 1.33 - 1.46: 147 1.46 - 1.59: 475 Bond restraints: 1710 Sorted by residual: bond pdb=" N LYS A 311 " pdb=" H LYS A 311 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N SER D 316 " pdb=" H SER D 316 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CD1 TYR E 310 " pdb=" HD1 TYR E 310 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CE1 TYR D 310 " pdb=" HE1 TYR D 310 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N LEU C 315 " pdb=" H LEU C 315 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 1705 not shown) Histogram of bond angle deviations from ideal: 70.77 - 83.77: 46 83.77 - 96.77: 8 96.77 - 109.78: 1403 109.78 - 122.78: 1583 122.78 - 135.78: 101 Bond angle restraints: 3141 Sorted by residual: angle pdb=" CA VAL H 313 " pdb=" CB VAL H 313 " pdb=" CG1 VAL H 313 " ideal model delta sigma weight residual 110.40 135.78 -25.38 1.70e+00 3.46e-01 2.23e+02 angle pdb=" CA VAL E 313 " pdb=" CB VAL E 313 " pdb=" CG1 VAL E 313 " ideal model delta sigma weight residual 110.40 133.04 -22.64 1.70e+00 3.46e-01 1.77e+02 angle pdb=" N VAL I 309 " pdb=" CA VAL I 309 " pdb=" HA VAL I 309 " ideal model delta sigma weight residual 110.00 70.77 39.23 3.00e+00 1.11e-01 1.71e+02 angle pdb=" N VAL D 309 " pdb=" CA VAL D 309 " pdb=" HA VAL D 309 " ideal model delta sigma weight residual 110.00 71.91 38.09 3.00e+00 1.11e-01 1.61e+02 angle pdb=" N VAL H 309 " pdb=" CA VAL H 309 " pdb=" HA VAL H 309 " ideal model delta sigma weight residual 110.00 72.16 37.84 3.00e+00 1.11e-01 1.59e+02 ... (remaining 3136 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.69: 703 17.69 - 35.37: 57 35.37 - 53.05: 9 53.05 - 70.73: 13 70.73 - 88.41: 10 Dihedral angle restraints: 792 sinusoidal: 459 harmonic: 333 Sorted by residual: dihedral pdb=" C VAL E 309 " pdb=" N VAL E 309 " pdb=" CA VAL E 309 " pdb=" CB VAL E 309 " ideal model delta harmonic sigma weight residual -122.00 -143.28 21.28 0 2.50e+00 1.60e-01 7.25e+01 dihedral pdb=" C VAL F 309 " pdb=" N VAL F 309 " pdb=" CA VAL F 309 " pdb=" CB VAL F 309 " ideal model delta harmonic sigma weight residual -122.00 -142.70 20.70 0 2.50e+00 1.60e-01 6.86e+01 dihedral pdb=" C VAL C 309 " pdb=" N VAL C 309 " pdb=" CA VAL C 309 " pdb=" CB VAL C 309 " ideal model delta harmonic sigma weight residual -122.00 -142.58 20.58 0 2.50e+00 1.60e-01 6.77e+01 ... (remaining 789 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.234: 104 0.234 - 0.467: 16 0.467 - 0.700: 2 0.700 - 0.934: 5 0.934 - 1.167: 8 Chirality restraints: 135 Sorted by residual: chirality pdb=" CB VAL F 313 " pdb=" CA VAL F 313 " pdb=" CG1 VAL F 313 " pdb=" CG2 VAL F 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.46 -1.17 2.00e-01 2.50e+01 3.40e+01 chirality pdb=" CB VAL D 313 " pdb=" CA VAL D 313 " pdb=" CG1 VAL D 313 " pdb=" CG2 VAL D 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.48 -1.15 2.00e-01 2.50e+01 3.32e+01 chirality pdb=" CB VAL H 313 " pdb=" CA VAL H 313 " pdb=" CG1 VAL H 313 " pdb=" CG2 VAL H 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.09 2.00e-01 2.50e+01 2.98e+01 ... (remaining 132 not shown) Planarity restraints: 207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 310 " 0.180 2.00e-02 2.50e+03 7.10e-02 1.51e+02 pdb=" CG TYR G 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR G 310 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR G 310 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR G 310 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR G 310 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR G 310 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 310 " 0.105 2.00e-02 2.50e+03 pdb=" HD1 TYR G 310 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR G 310 " -0.073 2.00e-02 2.50e+03 pdb=" HE1 TYR G 310 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR G 310 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 310 " 0.168 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG TYR H 310 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR H 310 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR H 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR H 310 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR H 310 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR H 310 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR H 310 " 0.115 2.00e-02 2.50e+03 pdb=" HD1 TYR H 310 " -0.011 2.00e-02 2.50e+03 pdb=" HD2 TYR H 310 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 TYR H 310 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR H 310 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.161 2.00e-02 2.50e+03 6.48e-02 1.26e+02 pdb=" CG TYR A 310 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.099 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.061 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.015 2.00e-02 2.50e+03 ... (remaining 204 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.13: 193 2.13 - 2.72: 2366 2.72 - 3.32: 4863 3.32 - 3.91: 5809 3.91 - 4.50: 7975 Nonbonded interactions: 21206 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.538 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.546 1.850 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.547 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.548 1.850 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.550 1.850 ... (remaining 21201 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.980 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: 0.030 Extract box with map and model: 3.320 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 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 : 0.013 0.049 819 Z= 0.835 Angle : 2.863 25.384 1098 Z= 1.799 Chirality : 0.342 1.167 135 Planarity : 0.023 0.081 126 Dihedral : 18.752 88.410 324 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Cbeta Deviations : 9.09 % 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: -1.61 (0.95), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.154 0.052 TYR G 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.156 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 41 average time/residue: 2.3719 time to fit residues: 98.1351 Evaluate side-chains 19 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.162 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.1874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.8857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 819 Z= 0.417 Angle : 1.558 11.032 1098 Z= 0.842 Chirality : 0.375 1.454 135 Planarity : 0.008 0.041 126 Dihedral : 7.848 18.706 99 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 6.06 % Allowed : 21.21 % Favored : 72.73 % 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: -1.35 (0.96), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 14 time to evaluate : 0.165 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 18 average time/residue: 1.9326 time to fit residues: 35.3179 Evaluate side-chains 13 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 11 time to evaluate : 0.164 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.8179 time to fit residues: 3.8590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 overall best weight: 0.5703 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.9708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 819 Z= 0.402 Angle : 1.512 11.077 1098 Z= 0.812 Chirality : 0.380 1.484 135 Planarity : 0.008 0.038 126 Dihedral : 6.354 12.174 99 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 7.07 % Allowed : 23.23 % Favored : 69.70 % 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: -1.31 (0.94), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 15 time to evaluate : 0.167 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 22 average time/residue: 1.7983 time to fit residues: 40.1789 Evaluate side-chains 11 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.8230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 1.0147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 819 Z= 0.406 Angle : 1.507 11.084 1098 Z= 0.810 Chirality : 0.380 1.484 135 Planarity : 0.008 0.037 126 Dihedral : 6.086 11.958 99 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.03 % Allowed : 30.30 % Favored : 66.67 % 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: -1.04 (0.97), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.74), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 10 time to evaluate : 0.239 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 13 average time/residue: 1.7998 time to fit residues: 23.8516 Evaluate side-chains 7 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.153 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 1.0485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 819 Z= 0.401 Angle : 1.495 11.065 1098 Z= 0.806 Chirality : 0.381 1.491 135 Planarity : 0.008 0.037 126 Dihedral : 6.048 11.906 99 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.01 % Allowed : 33.33 % Favored : 65.66 % 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: -0.93 (0.98), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.70 (0.75), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.181 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 8 average time/residue: 2.1597 time to fit residues: 17.6653 Evaluate side-chains 7 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 1.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 819 Z= 0.400 Angle : 1.491 11.224 1098 Z= 0.801 Chirality : 0.382 1.488 135 Planarity : 0.008 0.036 126 Dihedral : 5.774 11.248 99 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.01 % Allowed : 34.34 % Favored : 64.65 % 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: -0.78 (0.99), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.76), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.236 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 11 average time/residue: 1.0964 time to fit residues: 12.6116 Evaluate side-chains 8 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 1.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 819 Z= 0.399 Angle : 1.489 11.068 1098 Z= 0.800 Chirality : 0.381 1.483 135 Planarity : 0.008 0.036 126 Dihedral : 5.743 11.388 99 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.01 % Allowed : 34.34 % Favored : 64.65 % 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: -0.69 (1.00), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.51 (0.76), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR E 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.172 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 8 average time/residue: 1.2694 time to fit residues: 10.5575 Evaluate side-chains 7 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.180 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 1.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 819 Z= 0.401 Angle : 1.491 11.033 1098 Z= 0.803 Chirality : 0.380 1.482 135 Planarity : 0.008 0.036 126 Dihedral : 5.827 11.757 99 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.02 % Allowed : 33.33 % Favored : 64.65 % 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: -0.71 (1.00), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.77), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR H 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 6 time to evaluate : 0.169 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 8 average time/residue: 1.5717 time to fit residues: 12.9615 Evaluate side-chains 5 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.168 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 8 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: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 1.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 819 Z= 0.399 Angle : 1.481 11.018 1098 Z= 0.795 Chirality : 0.380 1.477 135 Planarity : 0.008 0.036 126 Dihedral : 5.632 11.244 99 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.02 % Allowed : 34.34 % Favored : 63.64 % 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: -0.65 (0.99), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.48 (0.75), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 9 time to evaluate : 0.164 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 11 average time/residue: 1.2820 time to fit residues: 14.5505 Evaluate side-chains 8 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.167 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9483 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 1.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 819 Z= 0.401 Angle : 1.497 10.919 1098 Z= 0.805 Chirality : 0.381 1.475 135 Planarity : 0.008 0.036 126 Dihedral : 5.676 11.699 99 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.01 % Allowed : 36.36 % Favored : 62.63 % 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: -0.69 (0.99), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.51 (0.76), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 162 Ramachandran restraints generated. 81 Oldfield, 0 Emsley, 81 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 5 time to evaluate : 0.182 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 1.4842 time to fit residues: 9.2389 Evaluate side-chains 5 residues out of total 99 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.9230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.233641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.227914 restraints weight = 2803.914| |-----------------------------------------------------------------------------| r_work (start): 0.5060 rms_B_bonded: 1.64 r_work: 0.5009 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.4948 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.4948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 1.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 819 Z= 0.400 Angle : 1.492 11.001 1098 Z= 0.802 Chirality : 0.381 1.478 135 Planarity : 0.008 0.036 126 Dihedral : 5.618 11.710 99 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 37.37 % Favored : 62.63 % 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: -0.82 (0.96), residues: 81 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.74), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1765.21 seconds wall clock time: 37 minutes 26.78 seconds (2246.78 seconds total)