Starting phenix.real_space_refine on Thu Jul 18 18:19:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/07_2024/8xoa_38524.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/07_2024/8xoa_38524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/07_2024/8xoa_38524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/07_2024/8xoa_38524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/07_2024/8xoa_38524.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/07_2024/8xoa_38524.cif" } resolution = 3.03 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= -0.002 sd= 0.100 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 26 5.16 5 C 1807 2.51 5 N 419 2.21 5 O 461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 399": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2713 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2700 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 23, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'WRF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.60, per 1000 atoms: 0.96 Number of scatterers: 2713 At special positions: 0 Unit cell: (52.7, 63.75, 69.7, 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 26 16.00 O 461 8.00 N 419 7.00 C 1807 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: 1.07 Conformation dependent library (CDL) restraints added in 767.9 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 676 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 93.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 19 through 49 removed outlier: 3.903A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 132 through 157 removed outlier: 4.323A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.913A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.674A pdb=" N GLY A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 269 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 323 removed outlier: 3.556A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 3.773A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.760A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.092A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.574A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 3.897A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 435 removed outlier: 3.686A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.769A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 720 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: 0.70 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 446 1.33 - 1.45: 682 1.45 - 1.57: 1605 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 2777 Sorted by residual: bond pdb=" N GLN A 271 " pdb=" CA GLN A 271 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.10e-03 1.98e+04 1.69e+01 bond pdb=" N ILE A 162 " pdb=" CA ILE A 162 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N ILE A 174 " pdb=" CA ILE A 174 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 9.95e+00 bond pdb=" N VAL A 269 " pdb=" CA VAL A 269 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.28e-02 6.10e+03 9.54e+00 ... (remaining 2772 not shown) Histogram of bond angle deviations from ideal: 95.91 - 103.53: 63 103.53 - 111.14: 1119 111.14 - 118.76: 1126 118.76 - 126.37: 1449 126.37 - 133.98: 38 Bond angle restraints: 3795 Sorted by residual: angle pdb=" N ASP A 262 " pdb=" CA ASP A 262 " pdb=" C ASP A 262 " ideal model delta sigma weight residual 111.28 105.93 5.35 1.09e+00 8.42e-01 2.41e+01 angle pdb=" CA GLN A 271 " pdb=" C GLN A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 118.09 122.14 -4.05 8.30e-01 1.45e+00 2.38e+01 angle pdb=" N LEU A 255 " pdb=" CA LEU A 255 " pdb=" C LEU A 255 " ideal model delta sigma weight residual 111.28 106.44 4.84 1.09e+00 8.42e-01 1.97e+01 angle pdb=" N PRO A 45 " pdb=" CA PRO A 45 " pdb=" C PRO A 45 " ideal model delta sigma weight residual 113.78 106.62 7.16 1.62e+00 3.81e-01 1.95e+01 angle pdb=" N LYS A 290 " pdb=" CA LYS A 290 " pdb=" C LYS A 290 " ideal model delta sigma weight residual 113.28 108.13 5.15 1.22e+00 6.72e-01 1.78e+01 ... (remaining 3790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.11: 1380 11.11 - 22.22: 159 22.22 - 33.32: 52 33.32 - 44.43: 13 44.43 - 55.54: 5 Dihedral angle restraints: 1609 sinusoidal: 549 harmonic: 1060 Sorted by residual: dihedral pdb=" C LYS A 290 " pdb=" N LYS A 290 " pdb=" CA LYS A 290 " pdb=" CB LYS A 290 " ideal model delta harmonic sigma weight residual -122.60 -110.21 -12.39 0 2.50e+00 1.60e-01 2.46e+01 dihedral pdb=" CA VAL A 417 " pdb=" C VAL A 417 " pdb=" N TYR A 418 " pdb=" CA TYR A 418 " ideal model delta harmonic sigma weight residual -180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE A 350 " pdb=" C ILE A 350 " pdb=" N LEU A 351 " pdb=" CA LEU A 351 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 1606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 397 0.075 - 0.150: 55 0.150 - 0.225: 11 0.225 - 0.300: 2 0.300 - 0.374: 2 Chirality restraints: 467 Sorted by residual: chirality pdb=" CA LYS A 290 " pdb=" N LYS A 290 " pdb=" C LYS A 290 " pdb=" CB LYS A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA ASP A 262 " pdb=" N ASP A 262 " pdb=" C ASP A 262 " pdb=" CB ASP A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA LEU A 255 " pdb=" N LEU A 255 " pdb=" C LEU A 255 " pdb=" CB LEU A 255 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 464 not shown) Planarity restraints: 468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 473 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO A 474 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 474 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 474 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 280 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C GLN A 280 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 280 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 281 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 44 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ILE A 44 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 44 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 45 " 0.011 2.00e-02 2.50e+03 ... (remaining 465 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 903 2.86 - 3.37: 2902 3.37 - 3.88: 4311 3.88 - 4.39: 5042 4.39 - 4.90: 8872 Nonbonded interactions: 22030 Sorted by model distance: nonbonded pdb=" NE2 GLN A 142 " pdb=" OD2 ASP A 426 " model vdw 2.346 2.520 nonbonded pdb=" O LEU A 30 " pdb=" ND2 ASN A 34 " model vdw 2.393 2.520 nonbonded pdb=" O SER A 180 " pdb=" OG SER A 180 " model vdw 2.452 2.440 nonbonded pdb=" O PRO A 473 " pdb=" CA PRO A 474 " model vdw 2.594 2.776 nonbonded pdb=" O ILE A 43 " pdb=" N TYR A 47 " model vdw 2.595 2.520 ... (remaining 22025 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.430 Find NCS groups from input model: 0.030 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 0.060 2777 Z= 0.441 Angle : 1.002 10.186 3795 Z= 0.662 Chirality : 0.061 0.374 467 Planarity : 0.007 0.056 468 Dihedral : 11.516 55.540 933 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.30 % 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: 0.90 (0.43), residues: 372 helix: 0.99 (0.30), residues: 304 sheet: None (None), residues: 0 loop : -0.93 (0.77), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.017 0.002 PHE A 238 TYR 0.012 0.002 TYR A 408 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.240 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1137 time to fit residues: 6.4873 Evaluate side-chains 39 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 0.0570 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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: 0.7404 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2777 Z= 0.187 Angle : 0.662 9.385 3795 Z= 0.314 Chirality : 0.040 0.121 467 Planarity : 0.006 0.049 468 Dihedral : 4.411 16.860 390 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.09 % Allowed : 7.64 % Favored : 91.27 % 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: 1.49 (0.43), residues: 372 helix: 1.33 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.63 (0.83), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.014 0.002 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.292 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.1136 time to fit residues: 6.8571 Evaluate side-chains 44 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 306 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2777 Z= 0.209 Angle : 0.646 9.399 3795 Z= 0.307 Chirality : 0.042 0.211 467 Planarity : 0.006 0.048 468 Dihedral : 4.286 17.108 390 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.45 % Allowed : 10.91 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.43), residues: 372 helix: 1.44 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.81 (0.82), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.020 0.002 PHE A 238 TYR 0.014 0.002 TYR A 422 ARG 0.005 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.292 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1131 time to fit residues: 6.7878 Evaluate side-chains 42 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7463 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2777 Z= 0.219 Angle : 0.647 9.411 3795 Z= 0.307 Chirality : 0.042 0.204 467 Planarity : 0.006 0.046 468 Dihedral : 4.258 17.293 390 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.09 % Allowed : 13.09 % Favored : 85.82 % 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: 1.56 (0.43), residues: 372 helix: 1.42 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.90 (0.80), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.019 0.002 PHE A 238 TYR 0.014 0.002 TYR A 422 ARG 0.005 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.260 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.0894 time to fit residues: 5.8327 Evaluate side-chains 47 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7483 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2777 Z= 0.236 Angle : 0.653 9.450 3795 Z= 0.312 Chirality : 0.042 0.152 467 Planarity : 0.006 0.045 468 Dihedral : 4.301 17.580 390 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.18 % Allowed : 13.45 % Favored : 84.36 % 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: 1.40 (0.43), residues: 372 helix: 1.31 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.97 (0.79), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.026 0.002 PHE A 238 TYR 0.015 0.002 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.285 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.1138 time to fit residues: 7.2913 Evaluate side-chains 48 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 34 optimal weight: 0.0470 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- 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: 0.7404 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2777 Z= 0.166 Angle : 0.608 9.404 3795 Z= 0.288 Chirality : 0.040 0.118 467 Planarity : 0.006 0.042 468 Dihedral : 4.053 15.862 390 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.45 % Allowed : 13.45 % Favored : 85.09 % 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: 1.92 (0.44), residues: 372 helix: 1.69 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.04 (0.80), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.002 PHE A 468 TYR 0.013 0.001 TYR A 422 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.286 Fit side-chains REVERT: A 319 MET cc_start: 0.7791 (mtt) cc_final: 0.7579 (mtt) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.0935 time to fit residues: 5.8298 Evaluate side-chains 47 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7441 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2777 Z= 0.199 Angle : 0.625 9.418 3795 Z= 0.296 Chirality : 0.041 0.129 467 Planarity : 0.006 0.043 468 Dihedral : 4.103 16.127 390 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.18 % Allowed : 13.09 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.43), residues: 372 helix: 1.62 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -1.02 (0.80), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.031 0.002 PHE A 238 TYR 0.014 0.002 TYR A 422 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.211 Fit side-chains REVERT: A 319 MET cc_start: 0.7857 (mtt) cc_final: 0.7652 (mtt) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.0979 time to fit residues: 6.3063 Evaluate side-chains 47 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.7427 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2777 Z= 0.188 Angle : 0.623 9.421 3795 Z= 0.295 Chirality : 0.042 0.235 467 Planarity : 0.006 0.043 468 Dihedral : 4.066 16.176 390 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.45 % Allowed : 14.55 % Favored : 84.00 % 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: 1.90 (0.43), residues: 372 helix: 1.66 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.96 (0.80), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.017 0.002 PHE A 468 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.287 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.1139 time to fit residues: 7.1054 Evaluate side-chains 46 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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: 0.7427 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2777 Z= 0.187 Angle : 0.627 9.405 3795 Z= 0.298 Chirality : 0.040 0.146 467 Planarity : 0.006 0.042 468 Dihedral : 4.071 16.060 390 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.09 % Allowed : 13.45 % Favored : 85.45 % 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: 1.91 (0.43), residues: 372 helix: 1.66 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.88 (0.81), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.014 0.001 PHE A 166 TYR 0.015 0.001 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.259 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.0982 time to fit residues: 5.9860 Evaluate side-chains 46 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.0040 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2777 Z= 0.193 Angle : 0.629 9.428 3795 Z= 0.298 Chirality : 0.041 0.158 467 Planarity : 0.006 0.043 468 Dihedral : 4.098 16.244 390 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.09 % Allowed : 13.45 % Favored : 85.45 % 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: 1.84 (0.43), residues: 372 helix: 1.62 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.93 (0.80), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.018 0.002 PHE A 468 TYR 0.015 0.001 TYR A 422 ARG 0.002 0.000 ARG A 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.273 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.0928 time to fit residues: 5.6795 Evaluate side-chains 46 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.0020 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.181414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.167343 restraints weight = 3315.945| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.29 r_work: 0.3663 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2777 Z= 0.202 Angle : 0.639 9.410 3795 Z= 0.305 Chirality : 0.041 0.166 467 Planarity : 0.006 0.043 468 Dihedral : 4.133 16.491 390 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.09 % Allowed : 14.18 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.43), residues: 372 helix: 1.57 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.84 (0.81), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.013 0.001 PHE A 27 TYR 0.015 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 955.26 seconds wall clock time: 21 minutes 16.03 seconds (1276.03 seconds total)