Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/11_2022/7dwv_30887.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/11_2022/7dwv_30887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/11_2022/7dwv_30887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/11_2022/7dwv_30887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/11_2022/7dwv_30887.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwv_30887/11_2022/7dwv_30887.pdb" } resolution = 3.07 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 "A GLU 200": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "F GLU 200": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2064 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "D" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "E" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "F" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Time building chain proxies: 1.53, per 1000 atoms: 0.74 Number of scatterers: 2064 At special positions: 0 Unit cell: (98.358, 84.162, 31.434, 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 30 16.00 O 402 8.00 N 354 7.00 C 1278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 214 " distance=2.02 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 214 " distance=2.02 Simple disulfide: pdb=" SG CYS D 179 " - pdb=" SG CYS D 214 " distance=2.02 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 214 " distance=2.02 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 214 " distance=2.03 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: 0.85 Conformation dependent library (CDL) restraints added in 298.5 milliseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 182 Processing sheet with id=AA2, first strand: chain 'D' and resid 180 through 182 8 hydrogen bonds defined for protein. 24 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: 0.36 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 672 1.34 - 1.45: 200 1.45 - 1.57: 1162 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 2082 Sorted by residual: bond pdb=" CB THR A 193 " pdb=" CG2 THR A 193 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB THR D 193 " pdb=" CG2 THR D 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 bond pdb=" CB THR C 193 " pdb=" CG2 THR C 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB THR F 193 " pdb=" CG2 THR F 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB THR E 193 " pdb=" CG2 THR E 193 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 ... (remaining 2077 not shown) Histogram of bond angle deviations from ideal: 100.34 - 106.54: 30 106.54 - 112.75: 1254 112.75 - 118.95: 535 118.95 - 125.15: 971 125.15 - 131.36: 12 Bond angle restraints: 2802 Sorted by residual: angle pdb=" N ASN C 181 " pdb=" CA ASN C 181 " pdb=" C ASN C 181 " ideal model delta sigma weight residual 107.93 112.24 -4.31 1.65e+00 3.67e-01 6.82e+00 angle pdb=" N ASN D 181 " pdb=" CA ASN D 181 " pdb=" C ASN D 181 " ideal model delta sigma weight residual 107.93 112.21 -4.28 1.65e+00 3.67e-01 6.74e+00 angle pdb=" N ASN F 181 " pdb=" CA ASN F 181 " pdb=" C ASN F 181 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.71e+00 angle pdb=" N ASN A 181 " pdb=" CA ASN A 181 " pdb=" C ASN A 181 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.70e+00 angle pdb=" N ASN B 181 " pdb=" CA ASN B 181 " pdb=" C ASN B 181 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.69e+00 ... (remaining 2797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.64: 984 11.64 - 23.29: 210 23.29 - 34.93: 90 34.93 - 46.57: 6 46.57 - 58.21: 6 Dihedral angle restraints: 1296 sinusoidal: 540 harmonic: 756 Sorted by residual: dihedral pdb=" CA MET C 206 " pdb=" C MET C 206 " pdb=" N GLU C 207 " pdb=" CA GLU C 207 " ideal model delta harmonic sigma weight residual -180.00 -165.64 -14.36 0 5.00e+00 4.00e-02 8.25e+00 dihedral pdb=" CA MET E 206 " pdb=" C MET E 206 " pdb=" N GLU E 207 " pdb=" CA GLU E 207 " ideal model delta harmonic sigma weight residual -180.00 -165.65 -14.35 0 5.00e+00 4.00e-02 8.24e+00 dihedral pdb=" CA MET A 206 " pdb=" C MET A 206 " pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta harmonic sigma weight residual -180.00 -165.65 -14.35 0 5.00e+00 4.00e-02 8.24e+00 ... (remaining 1293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 115 0.030 - 0.060: 127 0.060 - 0.091: 62 0.091 - 0.121: 32 0.121 - 0.151: 24 Chirality restraints: 360 Sorted by residual: chirality pdb=" CB THR C 183 " pdb=" CA THR C 183 " pdb=" OG1 THR C 183 " pdb=" CG2 THR C 183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CB THR A 183 " pdb=" CA THR A 183 " pdb=" OG1 THR A 183 " pdb=" CG2 THR A 183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CB THR D 183 " pdb=" CA THR D 183 " pdb=" OG1 THR D 183 " pdb=" CG2 THR D 183 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 357 not shown) Planarity restraints: 342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 187 " -0.009 2.00e-02 2.50e+03 9.09e-03 1.24e+00 pdb=" CG HIS C 187 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS C 187 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS C 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 187 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 187 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 187 " -0.010 2.00e-02 2.50e+03 9.07e-03 1.23e+00 pdb=" CG HIS E 187 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS E 187 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS E 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS E 187 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS E 187 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 187 " -0.009 2.00e-02 2.50e+03 8.96e-03 1.20e+00 pdb=" CG HIS B 187 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS B 187 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS B 187 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 187 " -0.004 2.00e-02 2.50e+03 ... (remaining 339 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 485 2.79 - 3.31: 2050 3.31 - 3.84: 3171 3.84 - 4.37: 3321 4.37 - 4.90: 7268 Nonbonded interactions: 16295 Sorted by model distance: nonbonded pdb=" OD1 ASN B 197 " pdb=" OG1 THR B 199 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASN A 197 " pdb=" OG1 THR A 199 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASN C 197 " pdb=" OG1 THR C 199 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASN F 197 " pdb=" OG1 THR F 199 " model vdw 2.258 2.440 nonbonded pdb=" OD1 ASN E 197 " pdb=" OG1 THR E 199 " model vdw 2.258 2.440 ... (remaining 16290 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' } 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 30 5.16 5 C 1278 2.51 5 N 354 2.21 5 O 402 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: 2.350 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: 12.250 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.020 Process input model: 11.800 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 0.055 2082 Z= 0.445 Angle : 0.799 4.308 2802 Z= 0.475 Chirality : 0.062 0.151 360 Planarity : 0.003 0.009 342 Dihedral : 14.691 58.214 774 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.83 % Favored : 73.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.45 (0.29), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.67 (0.22), residues: 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.215 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1206 time to fit residues: 9.2370 Evaluate side-chains 61 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS C 217 GLN D 212 GLN ** F 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2082 Z= 0.187 Angle : 0.575 5.146 2802 Z= 0.326 Chirality : 0.050 0.136 360 Planarity : 0.002 0.012 342 Dihedral : 5.255 11.508 258 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.17 % Favored : 76.83 % Rotamer Outliers : 11.90 % 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: -6.77 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.16 (0.26), residues: 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 64 time to evaluate : 0.268 Fit side-chains outliers start: 30 outliers final: 20 residues processed: 85 average time/residue: 0.1069 time to fit residues: 10.8603 Evaluate side-chains 82 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0235 time to fit residues: 1.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 2082 Z= 0.287 Angle : 0.681 4.451 2802 Z= 0.387 Chirality : 0.055 0.143 360 Planarity : 0.003 0.012 342 Dihedral : 5.867 13.859 258 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.02 % Favored : 73.98 % Rotamer Outliers : 13.49 % 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: -6.72 (0.33), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.11 (0.25), residues: 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 60 time to evaluate : 0.260 Fit side-chains outliers start: 34 outliers final: 26 residues processed: 85 average time/residue: 0.1023 time to fit residues: 10.5546 Evaluate side-chains 83 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 57 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.0245 time to fit residues: 1.4273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 212 GLN F 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2082 Z= 0.241 Angle : 0.665 4.229 2802 Z= 0.376 Chirality : 0.054 0.139 360 Planarity : 0.003 0.012 342 Dihedral : 5.601 14.818 258 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.98 % Favored : 76.02 % Rotamer Outliers : 5.16 % 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: -6.64 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.06 (0.26), residues: 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.263 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 0.1113 time to fit residues: 9.7520 Evaluate side-chains 69 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0234 time to fit residues: 0.7266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS F 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 2082 Z= 0.210 Angle : 0.626 4.355 2802 Z= 0.354 Chirality : 0.052 0.146 360 Planarity : 0.003 0.013 342 Dihedral : 5.364 15.509 258 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.80 % Favored : 75.20 % Rotamer Outliers : 8.73 % 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: -6.45 (0.35), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.91 (0.27), residues: 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 0.262 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 76 average time/residue: 0.1032 time to fit residues: 9.4626 Evaluate side-chains 79 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0244 time to fit residues: 1.1592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS F 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 2082 Z= 0.167 Angle : 0.599 4.756 2802 Z= 0.339 Chirality : 0.052 0.151 360 Planarity : 0.003 0.014 342 Dihedral : 4.885 15.479 258 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.14 % Favored : 78.86 % Rotamer Outliers : 3.97 % 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: -6.21 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.73 (0.29), residues: 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.275 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 71 average time/residue: 0.1096 time to fit residues: 9.3790 Evaluate side-chains 68 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.233 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0237 time to fit residues: 0.6491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS F 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2082 Z= 0.254 Angle : 0.681 5.546 2802 Z= 0.380 Chirality : 0.053 0.144 360 Planarity : 0.003 0.014 342 Dihedral : 5.495 16.821 258 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.02 % Favored : 73.98 % Rotamer Outliers : 4.76 % 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: -6.20 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.72 (0.29), residues: 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.267 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.0973 time to fit residues: 7.9004 Evaluate side-chains 68 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0232 time to fit residues: 0.7215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 HIS ** F 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 2082 Z= 0.340 Angle : 0.741 6.938 2802 Z= 0.413 Chirality : 0.056 0.141 360 Planarity : 0.003 0.013 342 Dihedral : 6.083 19.076 258 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.98 % Favored : 76.02 % Rotamer Outliers : 7.54 % 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: -6.28 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.78 (0.28), residues: 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 0.267 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 66 average time/residue: 0.1088 time to fit residues: 8.6289 Evaluate side-chains 70 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0257 time to fit residues: 0.9853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2082 Z= 0.265 Angle : 0.699 6.189 2802 Z= 0.393 Chirality : 0.053 0.140 360 Planarity : 0.003 0.014 342 Dihedral : 5.704 18.589 258 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.39 % Favored : 75.61 % Rotamer Outliers : 1.98 % 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: -6.20 (0.38), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.72 (0.29), residues: 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.260 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 0.1179 time to fit residues: 9.0961 Evaluate side-chains 60 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0344 time to fit residues: 0.4699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 14 optimal weight: 0.0470 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 2082 Z= 0.161 Angle : 0.627 5.063 2802 Z= 0.354 Chirality : 0.050 0.134 360 Planarity : 0.003 0.016 342 Dihedral : 4.828 15.798 258 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.11 % Favored : 80.89 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.00 (0.41), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.57 (0.31), residues: 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.238 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.1289 time to fit residues: 9.7539 Evaluate side-chains 61 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0318 time to fit residues: 0.4690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 HIS ** 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 = 0.4487 r_free = 0.4487 target = 0.139416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.130060 restraints weight = 3338.439| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 2.68 r_work: 0.4369 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4362 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work: 0.4354 rms_B_bonded: 2.53 restraints_weight: 0.1250 r_work: 0.4345 rms_B_bonded: 2.59 restraints_weight: 0.0625 r_work: 0.4336 rms_B_bonded: 2.68 restraints_weight: 0.0312 r_work: 0.4327 rms_B_bonded: 2.80 restraints_weight: 0.0156 r_work: 0.4317 rms_B_bonded: 2.93 restraints_weight: 0.0078 r_work: 0.4307 rms_B_bonded: 3.08 restraints_weight: 0.0039 r_work: 0.4297 rms_B_bonded: 3.25 restraints_weight: 0.0020 r_work: 0.4286 rms_B_bonded: 3.43 restraints_weight: 0.0010 r_work: 0.4274 rms_B_bonded: 3.64 restraints_weight: 0.0005 r_work: 0.4262 rms_B_bonded: 3.87 restraints_weight: 0.0002 r_work: 0.4249 rms_B_bonded: 4.12 restraints_weight: 0.0001 r_work: 0.4236 rms_B_bonded: 4.39 restraints_weight: 0.0001 r_work: 0.4222 rms_B_bonded: 4.68 restraints_weight: 0.0000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 2082 Z= 0.235 Angle : 0.676 5.570 2802 Z= 0.379 Chirality : 0.051 0.138 360 Planarity : 0.003 0.014 342 Dihedral : 5.324 16.659 258 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.17 % Favored : 76.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.96 (0.41), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.54 (0.31), residues: 246 =============================================================================== Job complete usr+sys time: 1217.16 seconds wall clock time: 22 minutes 30.80 seconds (1350.80 seconds total)