Starting phenix.real_space_refine on Thu Dec 7 16:15:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv4_32137/12_2023/7vv4_32137_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv4_32137/12_2023/7vv4_32137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv4_32137/12_2023/7vv4_32137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv4_32137/12_2023/7vv4_32137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv4_32137/12_2023/7vv4_32137_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vv4_32137/12_2023/7vv4_32137_updated.pdb" } resolution = 2.97 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= 0.003 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 S 18 5.16 5 C 1483 2.51 5 N 338 2.21 5 O 342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ASP 75": "OD1" <-> "OD2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 214": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2181 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2101 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.83, per 1000 atoms: 0.84 Number of scatterers: 2181 At special positions: 0 Unit cell: (66.276, 73.64, 61.016, 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 18 16.00 O 342 8.00 N 338 7.00 C 1483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.02 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: 0.93 Conformation dependent library (CDL) restraints added in 379.9 milliseconds 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'R' and resid 28 through 57 removed outlier: 3.691A pdb=" N ILE R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.657A pdb=" N LEU R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 94 removed outlier: 3.657A pdb=" N LEU R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 145 through 168 removed outlier: 3.508A pdb=" N GLU R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS R 168 " --> pdb=" O GLU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.898A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'R' and resid 237 through 243 Processing helix chain 'R' and resid 245 through 250 removed outlier: 3.503A pdb=" N ILE R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 258 removed outlier: 4.020A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 279 Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 281 through 284 No H-bonds generated for 'chain 'R' and resid 281 through 284' 146 hydrogen bonds defined for protein. 438 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: 0.64 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 400 1.33 - 1.45: 605 1.45 - 1.58: 1221 1.58 - 1.70: 1 1.70 - 1.82: 22 Bond restraints: 2249 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.621 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C HIS R 261 " pdb=" O HIS R 261 " ideal model delta sigma weight residual 1.244 1.217 0.027 9.80e-03 1.04e+04 7.64e+00 bond pdb=" C ASN R 271 " pdb=" O ASN R 271 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.89e+00 bond pdb=" N PHE R 76 " pdb=" CA PHE R 76 " ideal model delta sigma weight residual 1.459 1.432 0.027 1.19e-02 7.06e+03 5.26e+00 bond pdb=" C LEU R 267 " pdb=" O LEU R 267 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.15e-02 7.56e+03 5.19e+00 ... (remaining 2244 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.11: 15 103.11 - 110.82: 788 110.82 - 118.53: 960 118.53 - 126.24: 1251 126.24 - 133.95: 53 Bond angle restraints: 3067 Sorted by residual: angle pdb=" N LEU R 256 " pdb=" CA LEU R 256 " pdb=" C LEU R 256 " ideal model delta sigma weight residual 111.14 120.33 -9.19 1.08e+00 8.57e-01 7.24e+01 angle pdb=" N SER R 253 " pdb=" CA SER R 253 " pdb=" C SER R 253 " ideal model delta sigma weight residual 111.28 119.10 -7.82 1.09e+00 8.42e-01 5.14e+01 angle pdb=" N ILE R 260 " pdb=" CA ILE R 260 " pdb=" C ILE R 260 " ideal model delta sigma weight residual 110.72 117.16 -6.44 1.01e+00 9.80e-01 4.07e+01 angle pdb=" N ILE R 249 " pdb=" CA ILE R 249 " pdb=" C ILE R 249 " ideal model delta sigma weight residual 110.72 116.86 -6.14 1.01e+00 9.80e-01 3.70e+01 angle pdb=" N ILE R 246 " pdb=" CA ILE R 246 " pdb=" C ILE R 246 " ideal model delta sigma weight residual 110.72 116.82 -6.10 1.01e+00 9.80e-01 3.65e+01 ... (remaining 3062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.12: 1114 14.12 - 28.25: 139 28.25 - 42.37: 53 42.37 - 56.49: 8 56.49 - 70.61: 5 Dihedral angle restraints: 1319 sinusoidal: 542 harmonic: 777 Sorted by residual: dihedral pdb=" C PHE L 25 " pdb=" N PHE L 25 " pdb=" CA PHE L 25 " pdb=" CB PHE L 25 " ideal model delta harmonic sigma weight residual -122.60 -139.87 17.27 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" N PHE L 26 " pdb=" C PHE L 26 " pdb=" CA PHE L 26 " pdb=" CB PHE L 26 " ideal model delta harmonic sigma weight residual 122.80 139.84 -17.04 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" C PHE L 26 " pdb=" N PHE L 26 " pdb=" CA PHE L 26 " pdb=" CB PHE L 26 " ideal model delta harmonic sigma weight residual -122.60 -139.42 16.82 0 2.50e+00 1.60e-01 4.53e+01 ... (remaining 1316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 344 0.157 - 0.313: 13 0.313 - 0.470: 3 0.470 - 0.627: 1 0.627 - 0.783: 1 Chirality restraints: 362 Sorted by residual: chirality pdb=" CA PHE L 26 " pdb=" N PHE L 26 " pdb=" C PHE L 26 " pdb=" CB PHE L 26 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA PHE L 25 " pdb=" N PHE L 25 " pdb=" C PHE L 25 " pdb=" CB PHE L 25 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" CA HIS R 261 " pdb=" N HIS R 261 " pdb=" C HIS R 261 " pdb=" CB HIS R 261 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 ... (remaining 359 not shown) Planarity restraints: 356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 32 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO R 33 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 241 " -0.010 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C ILE R 241 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 241 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN R 242 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 30 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C THR R 30 " 0.022 2.00e-02 2.50e+03 pdb=" O THR R 30 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU R 31 " -0.007 2.00e-02 2.50e+03 ... (remaining 353 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 4 2.26 - 2.92: 869 2.92 - 3.58: 3276 3.58 - 4.24: 4697 4.24 - 4.90: 8095 Nonbonded interactions: 16941 Sorted by model distance: nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 1.600 2.440 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.237 2.440 nonbonded pdb=" OD1 ASP R 75 " pdb=" CB SER R 272 " model vdw 2.247 3.440 nonbonded pdb=" CB SER R 177 " pdb=" SG CYS L 22 " model vdw 2.259 3.800 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.309 2.440 ... (remaining 16936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.250 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: 0.950 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.650 Find NCS groups from input model: 0.060 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:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 0.086 2249 Z= 0.428 Angle : 1.197 12.523 3067 Z= 0.708 Chirality : 0.091 0.783 362 Planarity : 0.006 0.069 356 Dihedral : 14.733 70.611 812 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.75 % Allowed : 4.58 % Favored : 91.67 % Cbeta Deviations : 0.79 % 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: -0.53 (0.49), residues: 265 helix: 0.47 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -3.09 (0.60), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 250 HIS 0.004 0.002 HIS R 261 PHE 0.016 0.002 PHE L 26 TYR 0.011 0.003 TYR R 279 ARG 0.009 0.001 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.254 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 0.6223 time to fit residues: 33.6471 Evaluate side-chains 44 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1298 time to fit residues: 0.6184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.0010 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2249 Z= 0.182 Angle : 0.629 8.476 3067 Z= 0.295 Chirality : 0.041 0.314 362 Planarity : 0.004 0.050 356 Dihedral : 8.254 52.503 350 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.00 % Allowed : 15.00 % Favored : 80.00 % 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: 1.27 (0.52), residues: 265 helix: 1.92 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -3.23 (0.62), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 248 HIS 0.001 0.000 HIS R 261 PHE 0.017 0.001 PHE R 257 TYR 0.009 0.002 TYR R 113 ARG 0.002 0.000 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.268 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 0.6202 time to fit residues: 35.4881 Evaluate side-chains 45 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.240 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0678 time to fit residues: 0.4947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2249 Z= 0.207 Angle : 0.641 9.003 3067 Z= 0.294 Chirality : 0.042 0.307 362 Planarity : 0.003 0.043 356 Dihedral : 7.982 48.967 350 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.00 % Allowed : 19.17 % Favored : 75.83 % 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: 1.80 (0.53), residues: 265 helix: 2.30 (0.37), residues: 204 sheet: None (None), residues: 0 loop : -2.95 (0.63), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 PHE 0.013 0.001 PHE L 25 TYR 0.009 0.002 TYR R 113 ARG 0.003 0.000 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.223 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.6659 time to fit residues: 33.2413 Evaluate side-chains 50 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 6 average time/residue: 0.0698 time to fit residues: 0.8077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2249 Z= 0.189 Angle : 0.630 10.608 3067 Z= 0.286 Chirality : 0.041 0.303 362 Planarity : 0.003 0.039 356 Dihedral : 7.984 49.798 350 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.42 % Allowed : 24.17 % Favored : 70.42 % 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: 2.05 (0.53), residues: 265 helix: 2.40 (0.36), residues: 206 sheet: None (None), residues: 0 loop : -2.70 (0.66), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 PHE 0.020 0.001 PHE L 25 TYR 0.009 0.002 TYR R 222 ARG 0.002 0.000 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 50 time to evaluate : 0.246 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 57 average time/residue: 0.5774 time to fit residues: 34.3158 Evaluate side-chains 48 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.0990 time to fit residues: 0.7786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2249 Z= 0.174 Angle : 0.598 8.560 3067 Z= 0.275 Chirality : 0.042 0.299 362 Planarity : 0.003 0.038 356 Dihedral : 7.960 50.959 350 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.83 % Allowed : 26.67 % Favored : 67.50 % 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: 1.95 (0.53), residues: 265 helix: 2.41 (0.37), residues: 203 sheet: None (None), residues: 0 loop : -2.80 (0.63), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 PHE 0.023 0.001 PHE L 25 TYR 0.010 0.002 TYR R 222 ARG 0.002 0.000 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.234 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 50 average time/residue: 0.5819 time to fit residues: 30.3660 Evaluate side-chains 51 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.240 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 6 average time/residue: 0.0638 time to fit residues: 0.8117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2249 Z= 0.188 Angle : 0.611 7.935 3067 Z= 0.283 Chirality : 0.044 0.298 362 Planarity : 0.003 0.038 356 Dihedral : 8.049 52.465 350 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.33 % Allowed : 32.50 % Favored : 64.17 % 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: 1.99 (0.53), residues: 265 helix: 2.39 (0.37), residues: 203 sheet: None (None), residues: 0 loop : -2.60 (0.63), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP R 248 HIS 0.002 0.001 HIS R 261 PHE 0.024 0.001 PHE L 25 TYR 0.010 0.002 TYR R 222 ARG 0.002 0.000 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.239 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.6059 time to fit residues: 32.8269 Evaluate side-chains 49 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.243 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.0903 time to fit residues: 0.6539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 0.0670 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2249 Z= 0.185 Angle : 0.643 10.848 3067 Z= 0.291 Chirality : 0.044 0.294 362 Planarity : 0.003 0.038 356 Dihedral : 8.102 53.617 350 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.33 % Allowed : 32.08 % Favored : 64.58 % 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: 2.13 (0.54), residues: 265 helix: 2.50 (0.37), residues: 203 sheet: None (None), residues: 0 loop : -2.57 (0.63), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 248 HIS 0.002 0.001 HIS R 144 PHE 0.029 0.001 PHE L 25 TYR 0.010 0.002 TYR R 222 ARG 0.002 0.000 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.237 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.5983 time to fit residues: 31.1861 Evaluate side-chains 48 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.241 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0683 time to fit residues: 0.4973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.0670 chunk 10 optimal weight: 0.0670 chunk 18 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2249 Z= 0.153 Angle : 0.637 10.006 3067 Z= 0.288 Chirality : 0.043 0.284 362 Planarity : 0.003 0.038 356 Dihedral : 8.271 56.732 350 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.17 % Allowed : 31.25 % Favored : 64.58 % 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: 2.32 (0.54), residues: 265 helix: 2.61 (0.37), residues: 205 sheet: None (None), residues: 0 loop : -2.60 (0.64), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 154 HIS 0.002 0.001 HIS R 144 PHE 0.009 0.001 PHE R 76 TYR 0.008 0.002 TYR R 222 ARG 0.001 0.000 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.223 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 0.5841 time to fit residues: 35.3912 Evaluate side-chains 51 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.243 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 3 average time/residue: 0.0902 time to fit residues: 0.6130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2249 Z= 0.197 Angle : 0.661 9.713 3067 Z= 0.303 Chirality : 0.045 0.290 362 Planarity : 0.003 0.038 356 Dihedral : 8.226 56.368 350 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.89 % Favored : 97.74 % Rotamer: Outliers : 4.58 % Allowed : 32.08 % Favored : 63.33 % 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: 2.25 (0.53), residues: 265 helix: 2.60 (0.37), residues: 203 sheet: None (None), residues: 0 loop : -2.59 (0.64), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 248 HIS 0.002 0.001 HIS R 144 PHE 0.038 0.001 PHE L 25 TYR 0.009 0.002 TYR R 222 ARG 0.002 0.000 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.250 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 50 average time/residue: 0.5790 time to fit residues: 30.2451 Evaluate side-chains 50 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.227 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.0424 time to fit residues: 0.5185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 21 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2249 Z= 0.171 Angle : 0.670 9.696 3067 Z= 0.307 Chirality : 0.044 0.285 362 Planarity : 0.003 0.038 356 Dihedral : 8.362 58.372 350 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.89 % Favored : 97.74 % Rotamer: Outliers : 1.25 % Allowed : 35.42 % Favored : 63.33 % 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: 2.34 (0.54), residues: 265 helix: 2.71 (0.37), residues: 202 sheet: None (None), residues: 0 loop : -2.65 (0.63), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 154 HIS 0.002 0.001 HIS R 261 PHE 0.011 0.001 PHE R 183 TYR 0.009 0.002 TYR R 222 ARG 0.001 0.000 ARG R 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.231 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.6251 time to fit residues: 30.6423 Evaluate side-chains 48 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1804 time to fit residues: 0.5251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.0370 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.146726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.118411 restraints weight = 3182.836| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.76 r_work: 0.3564 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2249 Z= 0.172 Angle : 0.673 9.128 3067 Z= 0.308 Chirality : 0.045 0.281 362 Planarity : 0.003 0.038 356 Dihedral : 8.469 59.900 350 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.36 % Rotamer: Outliers : 1.67 % Allowed : 35.42 % Favored : 62.92 % 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: 2.23 (0.54), residues: 265 helix: 2.69 (0.38), residues: 199 sheet: None (None), residues: 0 loop : -2.63 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 154 HIS 0.002 0.001 HIS R 261 PHE 0.038 0.001 PHE L 25 TYR 0.009 0.002 TYR R 222 ARG 0.001 0.000 ARG R 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1212.81 seconds wall clock time: 22 minutes 42.14 seconds (1362.14 seconds total)