Starting phenix.real_space_refine on Sun Mar 10 14:31:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcc_37438/03_2024/8wcc_37438_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcc_37438/03_2024/8wcc_37438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcc_37438/03_2024/8wcc_37438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcc_37438/03_2024/8wcc_37438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcc_37438/03_2024/8wcc_37438_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcc_37438/03_2024/8wcc_37438_updated.pdb" } resolution = 3.04 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= -0.001 sd= 0.019 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 15 5.16 5 C 1376 2.51 5 N 325 2.21 5 O 340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2056 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2049 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'HAI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.83 Number of scatterers: 2056 At special positions: 0 Unit cell: (57.96, 72.68, 69, 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 15 16.00 O 340 8.00 N 325 7.00 C 1376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 359.3 milliseconds 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 514 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 9 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'R' and resid 24 through 49 removed outlier: 3.508A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS R 49 " --> pdb=" O ILE R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 84 Proline residue: R 77 - end of helix removed outlier: 3.756A pdb=" N VAL R 84 " --> pdb=" O MET R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 121 removed outlier: 4.201A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE R 111 " --> pdb=" O SER R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 No H-bonds generated for 'chain 'R' and resid 130 through 133' Processing helix chain 'R' and resid 136 through 160 Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 187 through 224 removed outlier: 3.944A pdb=" N VAL R 191 " --> pdb=" O LYS R 187 " (cutoff:3.500A) Proline residue: R 201 - end of helix removed outlier: 3.674A pdb=" N MET R 205 " --> pdb=" O PRO R 201 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG R 221 " --> pdb=" O LYS R 217 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 271 removed outlier: 3.592A pdb=" N PHE R 257 " --> pdb=" O MET R 253 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 280 through 302 removed outlier: 3.624A pdb=" N ASP R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU R 286 " --> pdb=" O LEU R 282 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR R 287 " --> pdb=" O ASN R 283 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP R 288 " --> pdb=" O ASP R 284 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 312 134 hydrogen bonds defined for protein. 402 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: 0.46 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 322 1.31 - 1.44: 622 1.44 - 1.57: 1138 1.57 - 1.69: 6 1.69 - 1.82: 24 Bond restraints: 2112 Sorted by residual: bond pdb=" CA SER R 182 " pdb=" C SER R 182 " ideal model delta sigma weight residual 1.524 1.453 0.071 8.10e-03 1.52e+04 7.68e+01 bond pdb=" CA ILE R 75 " pdb=" C ILE R 75 " ideal model delta sigma weight residual 1.524 1.443 0.081 1.23e-02 6.61e+03 4.34e+01 bond pdb=" CA LEU R 164 " pdb=" CB LEU R 164 " ideal model delta sigma weight residual 1.527 1.445 0.082 1.30e-02 5.92e+03 4.02e+01 bond pdb=" CA GLU R 169 " pdb=" C GLU R 169 " ideal model delta sigma weight residual 1.524 1.443 0.080 1.29e-02 6.01e+03 3.88e+01 bond pdb=" CA TYR R 305 " pdb=" C TYR R 305 " ideal model delta sigma weight residual 1.528 1.601 -0.073 1.18e-02 7.18e+03 3.84e+01 ... (remaining 2107 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.66: 69 104.66 - 112.17: 973 112.17 - 119.67: 884 119.67 - 127.18: 923 127.18 - 134.69: 31 Bond angle restraints: 2880 Sorted by residual: angle pdb=" N ASN R 163 " pdb=" CA ASN R 163 " pdb=" C ASN R 163 " ideal model delta sigma weight residual 112.04 97.79 14.25 1.44e+00 4.82e-01 9.80e+01 angle pdb=" N TYR R 305 " pdb=" CA TYR R 305 " pdb=" C TYR R 305 " ideal model delta sigma weight residual 109.93 120.73 -10.80 1.24e+00 6.50e-01 7.59e+01 angle pdb=" N GLU R 168 " pdb=" CA GLU R 168 " pdb=" C GLU R 168 " ideal model delta sigma weight residual 111.33 121.84 -10.51 1.21e+00 6.83e-01 7.54e+01 angle pdb=" N ILE R 47 " pdb=" CA ILE R 47 " pdb=" C ILE R 47 " ideal model delta sigma weight residual 111.44 122.98 -11.54 1.34e+00 5.57e-01 7.42e+01 angle pdb=" N GLU R 92 " pdb=" CA GLU R 92 " pdb=" C GLU R 92 " ideal model delta sigma weight residual 111.71 121.32 -9.61 1.15e+00 7.56e-01 6.98e+01 ... (remaining 2875 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 22.85: 1124 22.85 - 45.69: 81 45.69 - 68.53: 13 68.53 - 91.38: 2 91.38 - 114.22: 1 Dihedral angle restraints: 1221 sinusoidal: 428 harmonic: 793 Sorted by residual: dihedral pdb=" C LEU R 178 " pdb=" N LEU R 178 " pdb=" CA LEU R 178 " pdb=" CB LEU R 178 " ideal model delta harmonic sigma weight residual -122.60 -136.08 13.48 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" N LEU R 178 " pdb=" C LEU R 178 " pdb=" CA LEU R 178 " pdb=" CB LEU R 178 " ideal model delta harmonic sigma weight residual 122.80 136.08 -13.28 0 2.50e+00 1.60e-01 2.82e+01 dihedral pdb=" N PHE R 304 " pdb=" C PHE R 304 " pdb=" CA PHE R 304 " pdb=" CB PHE R 304 " ideal model delta harmonic sigma weight residual 122.80 109.67 13.13 0 2.50e+00 1.60e-01 2.76e+01 ... (remaining 1218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 239 0.115 - 0.230: 61 0.230 - 0.345: 27 0.345 - 0.460: 12 0.460 - 0.575: 4 Chirality restraints: 343 Sorted by residual: chirality pdb=" CA LEU R 178 " pdb=" N LEU R 178 " pdb=" C LEU R 178 " pdb=" CB LEU R 178 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.58 2.00e-01 2.50e+01 8.27e+00 chirality pdb=" CA MET R 76 " pdb=" N MET R 76 " pdb=" C MET R 76 " pdb=" CB MET R 76 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" CA ASP R 271 " pdb=" N ASP R 271 " pdb=" C ASP R 271 " pdb=" CB ASP R 271 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.29e+00 ... (remaining 340 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 76 " 0.086 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO R 77 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO R 77 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO R 77 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 165 " 0.025 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C LYS R 165 " -0.084 2.00e-02 2.50e+03 pdb=" O LYS R 165 " 0.031 2.00e-02 2.50e+03 pdb=" N GLY R 166 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 297 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO R 298 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO R 298 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO R 298 " -0.062 5.00e-02 4.00e+02 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1144 2.95 - 3.44: 2118 3.44 - 3.93: 3056 3.93 - 4.41: 3614 4.41 - 4.90: 5701 Nonbonded interactions: 15633 Sorted by model distance: nonbonded pdb=" N VAL R 84 " pdb=" N GLU R 85 " model vdw 2.464 2.560 nonbonded pdb=" O SER R 182 " pdb=" CA PRO R 183 " model vdw 2.467 2.776 nonbonded pdb=" N ASN R 135 " pdb=" O ASN R 135 " model vdw 2.489 2.496 nonbonded pdb=" N SER R 107 " pdb=" N ALA R 108 " model vdw 2.500 2.560 nonbonded pdb=" C SER R 189 " pdb=" OG SER R 189 " model vdw 2.517 2.616 ... (remaining 15628 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.370 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.017 0.088 2112 Z= 1.103 Angle : 2.047 14.252 2880 Z= 1.325 Chirality : 0.146 0.575 343 Planarity : 0.016 0.128 344 Dihedral : 16.414 114.218 707 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.87 % Allowed : 14.35 % Favored : 82.78 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.42), residues: 262 helix: -1.55 (0.31), residues: 189 sheet: None (None), residues: 0 loop : -3.84 (0.59), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP R 288 HIS 0.029 0.010 HIS R 62 PHE 0.068 0.006 PHE R 304 TYR 0.032 0.004 TYR R 287 ARG 0.012 0.002 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.209 Fit side-chains REVERT: R 278 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8293 (tp) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.1118 time to fit residues: 6.4657 Evaluate side-chains 39 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2112 Z= 0.310 Angle : 0.755 6.963 2880 Z= 0.387 Chirality : 0.044 0.143 343 Planarity : 0.008 0.067 344 Dihedral : 6.918 56.038 300 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.35 % Allowed : 17.70 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.49), residues: 262 helix: 0.57 (0.36), residues: 191 sheet: None (None), residues: 0 loop : -3.10 (0.61), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP R 88 HIS 0.004 0.001 HIS R 112 PHE 0.015 0.002 PHE R 304 TYR 0.006 0.001 TYR R 199 ARG 0.002 0.001 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.226 Fit side-chains REVERT: R 217 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8155 (tppt) REVERT: R 314 MET cc_start: 0.5742 (mmt) cc_final: 0.5427 (mmt) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 0.1482 time to fit residues: 8.9465 Evaluate side-chains 42 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 245 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2112 Z= 0.209 Angle : 0.627 6.561 2880 Z= 0.319 Chirality : 0.040 0.209 343 Planarity : 0.007 0.056 344 Dihedral : 4.496 16.769 295 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.44 % Allowed : 23.44 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.51), residues: 262 helix: 1.63 (0.37), residues: 191 sheet: None (None), residues: 0 loop : -2.81 (0.57), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 88 HIS 0.004 0.001 HIS R 112 PHE 0.009 0.001 PHE R 257 TYR 0.009 0.001 TYR R 130 ARG 0.002 0.000 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.218 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 44 average time/residue: 0.1428 time to fit residues: 7.4026 Evaluate side-chains 37 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.0370 chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.0050 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 0.3272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2112 Z= 0.194 Angle : 0.622 8.561 2880 Z= 0.306 Chirality : 0.040 0.210 343 Planarity : 0.006 0.049 344 Dihedral : 4.301 17.568 295 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.87 % Allowed : 22.01 % Favored : 75.12 % 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: 1.41 (0.51), residues: 262 helix: 1.97 (0.36), residues: 202 sheet: None (None), residues: 0 loop : -2.86 (0.58), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 88 HIS 0.004 0.001 HIS R 112 PHE 0.009 0.001 PHE R 257 TYR 0.006 0.001 TYR R 305 ARG 0.003 0.000 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.224 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.1288 time to fit residues: 6.5151 Evaluate side-chains 39 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 299 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2112 Z= 0.340 Angle : 0.667 6.203 2880 Z= 0.347 Chirality : 0.043 0.238 343 Planarity : 0.006 0.045 344 Dihedral : 4.729 18.100 295 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.31 % Allowed : 22.49 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.50), residues: 262 helix: 1.69 (0.36), residues: 194 sheet: None (None), residues: 0 loop : -2.53 (0.58), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 88 HIS 0.005 0.002 HIS R 112 PHE 0.015 0.001 PHE R 304 TYR 0.009 0.001 TYR R 287 ARG 0.003 0.001 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.264 Fit side-chains REVERT: R 128 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8172 (mp) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.1219 time to fit residues: 6.6773 Evaluate side-chains 41 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 299 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2112 Z= 0.293 Angle : 0.657 6.568 2880 Z= 0.332 Chirality : 0.042 0.250 343 Planarity : 0.006 0.044 344 Dihedral : 4.577 18.533 295 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.78 % Allowed : 21.05 % Favored : 74.16 % 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: 0.99 (0.51), residues: 262 helix: 1.69 (0.37), residues: 194 sheet: None (None), residues: 0 loop : -2.53 (0.58), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 88 HIS 0.004 0.001 HIS R 112 PHE 0.012 0.001 PHE R 304 TYR 0.013 0.001 TYR R 130 ARG 0.002 0.000 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.239 Fit side-chains REVERT: R 144 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6696 (mm) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.1056 time to fit residues: 5.8743 Evaluate side-chains 44 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 CYS Chi-restraints excluded: chain R residue 112 HIS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 245 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.0470 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2112 Z= 0.214 Angle : 0.613 5.777 2880 Z= 0.311 Chirality : 0.041 0.255 343 Planarity : 0.005 0.042 344 Dihedral : 4.337 18.250 295 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.78 % Allowed : 22.01 % Favored : 73.21 % 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: 1.29 (0.51), residues: 262 helix: 1.89 (0.37), residues: 195 sheet: None (None), residues: 0 loop : -2.41 (0.61), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 307 HIS 0.005 0.001 HIS R 112 PHE 0.010 0.001 PHE R 257 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.220 Fit side-chains REVERT: R 144 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6622 (mm) REVERT: R 310 ARG cc_start: 0.6962 (tmm160) cc_final: 0.6713 (tpp80) outliers start: 10 outliers final: 8 residues processed: 44 average time/residue: 0.1225 time to fit residues: 6.5048 Evaluate side-chains 45 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 CYS Chi-restraints excluded: chain R residue 107 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 299 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.0000 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2112 Z= 0.208 Angle : 0.612 7.302 2880 Z= 0.308 Chirality : 0.041 0.263 343 Planarity : 0.005 0.039 344 Dihedral : 4.148 17.900 295 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.26 % Allowed : 23.44 % Favored : 71.29 % 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: 1.42 (0.51), residues: 262 helix: 2.02 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -2.73 (0.53), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 307 HIS 0.003 0.001 HIS R 112 PHE 0.014 0.001 PHE R 184 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.000 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.212 Fit side-chains REVERT: R 144 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6588 (mm) REVERT: R 310 ARG cc_start: 0.6873 (tmm160) cc_final: 0.6661 (tpp80) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 0.1419 time to fit residues: 7.9611 Evaluate side-chains 43 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 CYS Chi-restraints excluded: chain R residue 112 HIS Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 299 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.0270 chunk 13 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2112 Z= 0.216 Angle : 0.599 5.825 2880 Z= 0.306 Chirality : 0.041 0.276 343 Planarity : 0.005 0.039 344 Dihedral : 4.164 18.076 295 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.78 % Allowed : 24.40 % Favored : 70.81 % 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: 1.44 (0.51), residues: 262 helix: 2.03 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -2.71 (0.54), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 147 HIS 0.003 0.001 HIS R 112 PHE 0.013 0.001 PHE R 184 TYR 0.009 0.001 TYR R 130 ARG 0.003 0.001 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.226 Fit side-chains REVERT: R 144 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6618 (mm) outliers start: 10 outliers final: 8 residues processed: 43 average time/residue: 0.1260 time to fit residues: 6.5293 Evaluate side-chains 43 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 CYS Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 135 ASN Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 299 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 14 optimal weight: 0.0170 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2112 Z= 0.203 Angle : 0.611 7.725 2880 Z= 0.305 Chirality : 0.041 0.284 343 Planarity : 0.005 0.038 344 Dihedral : 4.081 17.986 295 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.31 % Allowed : 24.40 % Favored : 71.29 % 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: 1.58 (0.52), residues: 262 helix: 2.12 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -2.61 (0.55), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 147 HIS 0.003 0.001 HIS R 112 PHE 0.013 0.001 PHE R 184 TYR 0.008 0.001 TYR R 130 ARG 0.003 0.001 ARG R 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.209 Fit side-chains REVERT: R 142 MET cc_start: 0.7700 (mtt) cc_final: 0.7416 (mtp) REVERT: R 144 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6595 (mm) outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.1279 time to fit residues: 6.5850 Evaluate side-chains 45 residues out of total 239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 CYS Chi-restraints excluded: chain R residue 112 HIS Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 135 ASN Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 299 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.0000 chunk 25 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 overall best weight: 0.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 40 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.117223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.107480 restraints weight = 4084.182| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.46 r_work: 0.3575 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2112 Z= 0.177 Angle : 0.586 5.950 2880 Z= 0.295 Chirality : 0.040 0.280 343 Planarity : 0.005 0.038 344 Dihedral : 3.953 17.805 295 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.31 % Allowed : 24.88 % Favored : 70.81 % 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 (0.52), residues: 262 helix: 2.32 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -2.13 (0.61), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 147 HIS 0.003 0.001 HIS R 112 PHE 0.012 0.001 PHE R 184 TYR 0.007 0.001 TYR R 130 ARG 0.003 0.001 ARG R 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1016.07 seconds wall clock time: 18 minutes 48.80 seconds (1128.80 seconds total)