Starting phenix.real_space_refine on Mon Jun 24 14:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/06_2024/8xoa_38524_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/06_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_38524/06_2024/8xoa_38524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/06_2024/8xoa_38524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/06_2024/8xoa_38524_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/06_2024/8xoa_38524_updated.pdb" } 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-5370/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: 2.44, per 1000 atoms: 0.90 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: 0.97 Conformation dependent library (CDL) restraints added in 664.5 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... running ksdssp... Secondary structure from input PDB file: 15 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 20 through 48 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 156 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 178 Processing helix chain 'A' and resid 182 through 210 Processing helix chain 'A' and resid 214 through 245 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 250 through 268 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 292 through 322 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 327 through 333 removed outlier: 3.760A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 355 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 357 through 377 Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 381 through 413 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 419 through 434 removed outlier: 3.686A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 449 through 470 Proline residue: A 465 - end of helix removed outlier: 4.169A pdb=" N PHE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE A 469 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 651 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: 0.71 Time building geometry restraints manager: 1.08 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: 908 2.86 - 3.37: 2923 3.37 - 3.88: 4343 3.88 - 4.39: 5083 4.39 - 4.90: 8877 Nonbonded interactions: 22134 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 22129 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: 0.710 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: 0.010 Extract box with map and model: 3.480 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.880 Find NCS groups from input model: 0.080 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- 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= 0.416 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 : 0.290 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1180 time to fit residues: 6.7888 Evaluate side-chains 39 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.0070 chunk 33 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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: 0.7449 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2777 Z= 0.210 Angle : 0.667 9.294 3795 Z= 0.313 Chirality : 0.041 0.123 467 Planarity : 0.006 0.050 468 Dihedral : 4.435 17.118 390 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.09 % Allowed : 9.09 % Favored : 89.82 % 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: 1.22 (0.43), residues: 372 helix: 1.12 (0.29), residues: 311 sheet: None (None), residues: 0 loop : -0.42 (0.84), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.016 0.002 PHE A 238 TYR 0.012 0.002 TYR A 422 ARG 0.002 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 : 0.297 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.1179 time to fit residues: 6.9472 Evaluate side-chains 43 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 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: 0.7460 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2777 Z= 0.205 Angle : 0.632 9.327 3795 Z= 0.298 Chirality : 0.041 0.220 467 Planarity : 0.006 0.047 468 Dihedral : 4.272 16.840 390 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.45 % Allowed : 11.64 % Favored : 86.91 % 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: 1.39 (0.44), residues: 372 helix: 1.25 (0.29), residues: 310 sheet: None (None), residues: 0 loop : -0.47 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.016 0.002 PHE A 238 TYR 0.012 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 48 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.281 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.1155 time to fit residues: 6.7750 Evaluate side-chains 43 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 0.0670 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.7453 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2777 Z= 0.197 Angle : 0.621 9.356 3795 Z= 0.294 Chirality : 0.041 0.213 467 Planarity : 0.006 0.045 468 Dihedral : 4.182 16.478 390 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.18 % Allowed : 11.64 % Favored : 86.18 % 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 (0.44), residues: 372 helix: 1.31 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.43 (0.89), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.024 0.002 PHE A 238 TYR 0.012 0.002 TYR A 422 ARG 0.002 0.000 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 49 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.276 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.1130 time to fit residues: 6.9500 Evaluate side-chains 42 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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: 0.5980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7471 moved from start: 0.1503 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= 0.214 Angle : 0.636 9.357 3795 Z= 0.300 Chirality : 0.041 0.125 467 Planarity : 0.006 0.044 468 Dihedral : 4.195 16.512 390 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.18 % Allowed : 12.36 % 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: 1.40 (0.43), residues: 372 helix: 1.25 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.47 (0.88), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.013 0.001 PHE A 27 TYR 0.013 0.002 TYR A 422 ARG 0.003 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 48 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.251 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.0992 time to fit residues: 5.8291 Evaluate side-chains 45 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 323 MET Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7465 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2777 Z= 0.204 Angle : 0.620 9.387 3795 Z= 0.293 Chirality : 0.040 0.125 467 Planarity : 0.006 0.043 468 Dihedral : 4.134 16.331 390 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.82 % Allowed : 12.73 % 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: 1.45 (0.44), residues: 372 helix: 1.29 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.50 (0.88), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 358 HIS 0.001 0.001 HIS A 414 PHE 0.030 0.002 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.002 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 44 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.313 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 42 average time/residue: 0.1086 time to fit residues: 6.0990 Evaluate side-chains 44 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 323 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: 0.8980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7477 moved from start: 0.1734 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= 0.214 Angle : 0.628 9.419 3795 Z= 0.297 Chirality : 0.041 0.139 467 Planarity : 0.006 0.044 468 Dihedral : 4.167 16.408 390 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.55 % Allowed : 11.64 % 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: 1.40 (0.43), residues: 372 helix: 1.23 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.36 (0.88), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.014 0.002 PHE A 166 TYR 0.013 0.002 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** 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 49 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.278 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.1152 time to fit residues: 6.7319 Evaluate side-chains 43 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 323 MET 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: 0.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 28 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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: 0.7466 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2777 Z= 0.202 Angle : 0.620 9.421 3795 Z= 0.293 Chirality : 0.040 0.155 467 Planarity : 0.006 0.043 468 Dihedral : 4.115 16.203 390 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.82 % Allowed : 12.36 % 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: 1.47 (0.44), residues: 372 helix: 1.29 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.43 (0.87), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.013 0.001 PHE A 27 TYR 0.013 0.002 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** 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 44 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.282 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.1010 time to fit residues: 5.6218 Evaluate side-chains 42 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 323 MET 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: 1.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 31 optimal weight: 0.2980 chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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: 0.7397 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2777 Z= 0.162 Angle : 0.598 9.370 3795 Z= 0.282 Chirality : 0.039 0.159 467 Planarity : 0.006 0.042 468 Dihedral : 3.929 14.907 390 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.73 % Allowed : 14.18 % 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: 1.89 (0.44), residues: 372 helix: 1.61 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -0.54 (0.86), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.015 0.001 PHE A 166 TYR 0.012 0.001 TYR A 422 ARG 0.003 0.000 ARG A 217 *********************** 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 43 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.281 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.1027 time to fit residues: 5.8779 Evaluate side-chains 43 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.0060 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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: 0.7403 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2777 Z= 0.171 Angle : 0.609 9.370 3795 Z= 0.286 Chirality : 0.040 0.168 467 Planarity : 0.006 0.043 468 Dihedral : 3.907 14.601 390 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.09 % Allowed : 14.55 % 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: 1.97 (0.44), residues: 372 helix: 1.67 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.56 (0.86), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.014 0.001 PHE A 27 TYR 0.014 0.001 TYR A 422 ARG 0.001 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 45 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.299 Fit side-chains REVERT: A 319 MET cc_start: 0.7894 (mtt) cc_final: 0.7691 (mtt) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.1026 time to fit residues: 6.1278 Evaluate side-chains 43 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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: 0.1980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.186779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.172891 restraints weight = 3268.899| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.28 r_work: 0.3818 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2107 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= 0.183 Angle : 0.616 9.367 3795 Z= 0.289 Chirality : 0.040 0.172 467 Planarity : 0.006 0.043 468 Dihedral : 3.926 14.901 390 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.45 % Allowed : 15.27 % Favored : 83.27 % 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: 1.90 (0.44), residues: 372 helix: 1.63 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.59 (0.86), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.014 0.001 PHE A 27 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 956.68 seconds wall clock time: 18 minutes 3.03 seconds (1083.03 seconds total)