Starting phenix.real_space_refine on Mon Sep 23 12:51:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/09_2024/8xoa_38524.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/09_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_38524/09_2024/8xoa_38524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/09_2024/8xoa_38524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/09_2024/8xoa_38524.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xoa_38524/09_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. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 2.51, per 1000 atoms: 0.93 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 - 3.00 Amino acid : True - 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: 0.72 Conformation dependent library (CDL) restraints added in 327.0 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: 0.25 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: 0.85 Time building geometry restraints manager: 0.81 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: 0.00 - 2.04: 3581 2.04 - 4.07: 182 4.07 - 6.11: 24 6.11 - 8.15: 5 8.15 - 10.19: 3 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 3.120 nonbonded pdb=" O LEU A 30 " pdb=" ND2 ASN A 34 " model vdw 2.393 3.120 nonbonded pdb=" O SER A 180 " pdb=" OG SER A 180 " model vdw 2.452 3.040 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 3.120 ... (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: 0.750 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.950 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- 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 : 0.262 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1142 time to fit residues: 6.5709 Evaluate side-chains 39 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 33 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: 0.7423 moved from start: 0.1064 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= 0.202 Angle : 0.677 9.423 3795 Z= 0.322 Chirality : 0.041 0.123 467 Planarity : 0.006 0.050 468 Dihedral : 4.488 17.163 390 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.09 % Allowed : 8.73 % Favored : 90.18 % 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: 1.37 (0.43), residues: 372 helix: 1.24 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.62 (0.85), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.002 PHE A 238 TYR 0.015 0.002 TYR A 422 ARG 0.002 0.001 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 48 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.270 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.1214 time to fit residues: 7.1022 Evaluate side-chains 42 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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: 0.3980 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7417 moved from start: 0.1368 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= 0.189 Angle : 0.636 9.431 3795 Z= 0.302 Chirality : 0.041 0.202 467 Planarity : 0.006 0.047 468 Dihedral : 4.248 16.572 390 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.82 % Allowed : 10.55 % 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: 1.82 (0.44), residues: 372 helix: 1.59 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.74 (0.83), residues: 58 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 0.018 0.002 PHE A 238 TYR 0.013 0.002 TYR A 422 ARG 0.003 0.000 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 54 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.286 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.1114 time to fit residues: 7.2535 Evaluate side-chains 45 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 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 306 MET Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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: 0.7460 moved from start: 0.1581 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= 0.219 Angle : 0.653 9.394 3795 Z= 0.311 Chirality : 0.042 0.220 467 Planarity : 0.006 0.045 468 Dihedral : 4.275 17.013 390 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.31 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: 1.62 (0.43), residues: 372 helix: 1.47 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.92 (0.81), residues: 57 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 0.020 0.002 PHE A 238 TYR 0.014 0.002 TYR A 422 ARG 0.004 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 53 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.310 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.1017 time to fit residues: 7.0469 Evaluate side-chains 48 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2777 Z= 0.225 Angle : 0.654 9.457 3795 Z= 0.313 Chirality : 0.042 0.145 467 Planarity : 0.006 0.045 468 Dihedral : 4.282 17.319 390 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 1.45 (0.43), residues: 372 helix: 1.36 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -1.05 (0.79), residues: 57 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 0.025 0.002 PHE A 238 TYR 0.015 0.002 TYR A 422 ARG 0.002 0.001 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 52 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.282 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.0964 time to fit residues: 6.3125 Evaluate side-chains 49 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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=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: 0.5980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.0770 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.2834 ------------------------------------------------------------------------------- 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: 0.7383 moved from start: 0.1961 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= 0.163 Angle : 0.606 9.379 3795 Z= 0.289 Chirality : 0.040 0.121 467 Planarity : 0.005 0.042 468 Dihedral : 4.006 15.434 390 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 2.06 (0.44), residues: 372 helix: 1.78 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.02 (0.82), residues: 55 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 468 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 49 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.268 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.1201 time to fit residues: 7.3647 Evaluate side-chains 44 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.0770 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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: 0.7444 moved from start: 0.1966 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= 0.207 Angle : 0.638 9.425 3795 Z= 0.303 Chirality : 0.041 0.136 467 Planarity : 0.006 0.043 468 Dihedral : 4.128 16.109 390 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.45 % Allowed : 13.09 % 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: 1.82 (0.43), residues: 372 helix: 1.60 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.00 (0.82), residues: 55 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 0.031 0.002 PHE A 238 TYR 0.015 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 48 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.264 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.1053 time to fit residues: 6.5291 Evaluate side-chains 45 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.0060 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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: 0.7425 moved from start: 0.2021 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 : 0.623 9.416 3795 Z= 0.296 Chirality : 0.040 0.140 467 Planarity : 0.006 0.042 468 Dihedral : 4.083 16.149 390 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.73 % Allowed : 14.55 % 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: 1.88 (0.43), residues: 372 helix: 1.65 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.97 (0.82), residues: 55 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 0.001 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 46 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.309 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.1047 time to fit residues: 6.4465 Evaluate side-chains 45 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 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 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: 2.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7446 moved from start: 0.2026 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= 0.204 Angle : 0.640 9.426 3795 Z= 0.305 Chirality : 0.041 0.148 467 Planarity : 0.006 0.043 468 Dihedral : 4.138 16.450 390 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.82 % Allowed : 13.45 % 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: 1.58 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.92 (0.83), residues: 55 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 0.016 0.002 PHE A 166 TYR 0.015 0.002 TYR A 422 ARG 0.001 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 48 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.278 Fit side-chains REVERT: A 334 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6827 (m-80) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.1002 time to fit residues: 6.2389 Evaluate side-chains 47 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 334 PHE 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: 0.8980 chunk 17 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 31 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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: 0.7396 moved from start: 0.2171 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= 0.172 Angle : 0.616 9.436 3795 Z= 0.293 Chirality : 0.040 0.156 467 Planarity : 0.006 0.042 468 Dihedral : 4.014 15.642 390 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.45 % Allowed : 14.91 % Favored : 83.64 % 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: 2.16 (0.44), residues: 372 helix: 1.81 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -0.76 (0.83), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.016 0.001 PHE A 468 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 ********************** 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 47 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.301 Fit side-chains REVERT: A 334 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6726 (m-80) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1023 time to fit residues: 6.4134 Evaluate side-chains 47 residues out of total 302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 334 PHE 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 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4350 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.183337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.169173 restraints weight = 3310.011| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.30 r_work: 0.3790 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2182 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= 0.177 Angle : 0.626 9.404 3795 Z= 0.298 Chirality : 0.040 0.161 467 Planarity : 0.006 0.042 468 Dihedral : 4.002 15.328 390 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.82 % Allowed : 14.55 % Favored : 83.64 % 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: 2.17 (0.44), residues: 372 helix: 1.81 (0.29), residues: 318 sheet: None (None), residues: 0 loop : -0.71 (0.84), residues: 54 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 0.001 PHE A 166 TYR 0.015 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: 1012.02 seconds wall clock time: 18 minutes 37.94 seconds (1117.94 seconds total)