Starting phenix.real_space_refine on Fri Apr 5 13:24:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/04_2024/8jta_36638_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/04_2024/8jta_36638.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/04_2024/8jta_36638_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/04_2024/8jta_36638_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/04_2024/8jta_36638_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/04_2024/8jta_36638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/04_2024/8jta_36638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/04_2024/8jta_36638_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/04_2024/8jta_36638_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.050 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 24 5.16 5 C 1923 2.51 5 N 445 2.21 5 O 487 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 TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2879 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2856 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 23, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'YHL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.71 Number of scatterers: 2879 At special positions: 0 Unit cell: (53.55, 68.85, 83.3, 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 24 16.00 O 487 8.00 N 445 7.00 C 1923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 545.4 milliseconds 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 0 sheets defined 76.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 20 through 43 removed outlier: 4.040A pdb=" N ASP A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 129 through 156 removed outlier: 3.503A pdb=" N LEU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.785A pdb=" N GLY A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.643A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 210 Processing helix chain 'A' and resid 214 through 245 removed outlier: 4.197A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.518A pdb=" N SER A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 269 removed outlier: 3.618A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 292 through 312 removed outlier: 3.790A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.879A pdb=" N SER A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.564A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 413 removed outlier: 4.295A pdb=" N ALA A 386 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Proline residue: A 387 - end of helix removed outlier: 3.502A pdb=" N GLY A 392 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER A 400 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET A 403 " --> pdb=" O SER A 400 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 419 through 446 removed outlier: 3.756A pdb=" N ALA A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.545A pdb=" N GLY A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 468 removed outlier: 3.960A pdb=" N ILE A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Proline residue: A 465 - end of helix removed outlier: 4.729A pdb=" N PHE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 477 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: 0.77 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 438 1.31 - 1.43: 749 1.43 - 1.56: 1718 1.56 - 1.68: 3 1.68 - 1.81: 41 Bond restraints: 2949 Sorted by residual: bond pdb=" C10 YHL A 501 " pdb=" C9 YHL A 501 " ideal model delta sigma weight residual 1.510 1.225 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C8 YHL A 501 " pdb=" C9 YHL A 501 " ideal model delta sigma weight residual 1.487 1.271 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C16 YHL A 501 " pdb=" C17 YHL A 501 " ideal model delta sigma weight residual 1.527 1.349 0.178 2.00e-02 2.50e+03 7.92e+01 bond pdb=" C10 YHL A 501 " pdb=" C11 YHL A 501 " ideal model delta sigma weight residual 1.402 1.575 -0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" C13 YHL A 501 " pdb=" C14 YHL A 501 " ideal model delta sigma weight residual 1.389 1.218 0.171 2.00e-02 2.50e+03 7.34e+01 ... (remaining 2944 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.97: 103 105.97 - 113.05: 1567 113.05 - 120.12: 1186 120.12 - 127.20: 1129 127.20 - 134.27: 35 Bond angle restraints: 4020 Sorted by residual: angle pdb=" N LEU A 470 " pdb=" CA LEU A 470 " pdb=" C LEU A 470 " ideal model delta sigma weight residual 114.56 99.49 15.07 1.27e+00 6.20e-01 1.41e+02 angle pdb=" C6 YHL A 501 " pdb=" N7 YHL A 501 " pdb=" C8 YHL A 501 " ideal model delta sigma weight residual 104.16 132.85 -28.69 3.00e+00 1.11e-01 9.15e+01 angle pdb=" N PRO A 473 " pdb=" CA PRO A 473 " pdb=" C PRO A 473 " ideal model delta sigma weight residual 110.70 119.23 -8.53 1.22e+00 6.72e-01 4.89e+01 angle pdb=" N LEU A 470 " pdb=" CA LEU A 470 " pdb=" CB LEU A 470 " ideal model delta sigma weight residual 111.00 118.47 -7.47 1.33e+00 5.65e-01 3.16e+01 angle pdb=" N PHE A 469 " pdb=" CA PHE A 469 " pdb=" C PHE A 469 " ideal model delta sigma weight residual 108.52 98.90 9.62 1.74e+00 3.30e-01 3.06e+01 ... (remaining 4015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1549 17.96 - 35.92: 138 35.92 - 53.88: 31 53.88 - 71.84: 4 71.84 - 89.79: 1 Dihedral angle restraints: 1723 sinusoidal: 631 harmonic: 1092 Sorted by residual: dihedral pdb=" C ILE A 367 " pdb=" N ILE A 367 " pdb=" CA ILE A 367 " pdb=" CB ILE A 367 " ideal model delta harmonic sigma weight residual -122.00 -130.92 8.92 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" CB GLU A 312 " pdb=" CG GLU A 312 " pdb=" CD GLU A 312 " pdb=" OE1 GLU A 312 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" C PHE A 303 " pdb=" N PHE A 303 " pdb=" CA PHE A 303 " pdb=" CB PHE A 303 " ideal model delta harmonic sigma weight residual -122.60 -130.61 8.01 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 1720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 372 0.076 - 0.151: 91 0.151 - 0.226: 18 0.226 - 0.302: 2 0.302 - 0.377: 1 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA PHE A 469 " pdb=" N PHE A 469 " pdb=" C PHE A 469 " pdb=" CB PHE A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA LEU A 342 " pdb=" N LEU A 342 " pdb=" C LEU A 342 " pdb=" CB LEU A 342 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE A 343 " pdb=" N ILE A 343 " pdb=" C ILE A 343 " pdb=" CB ILE A 343 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 481 not shown) Planarity restraints: 492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 336 " 0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PRO A 336 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO A 336 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 337 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 375 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO A 376 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 343 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C ILE A 343 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 343 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY A 344 " 0.014 2.00e-02 2.50e+03 ... (remaining 489 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 997 2.84 - 3.35: 2996 3.35 - 3.87: 4633 3.87 - 4.38: 5106 4.38 - 4.90: 8519 Nonbonded interactions: 22251 Sorted by model distance: nonbonded pdb=" O SER A 18 " pdb=" OG SER A 18 " model vdw 2.320 2.440 nonbonded pdb=" O PHE A 176 " pdb=" OG SER A 179 " model vdw 2.420 2.440 nonbonded pdb=" O ILE A 194 " pdb=" OG SER A 197 " model vdw 2.459 2.440 nonbonded pdb=" N LEU A 470 " pdb=" N ARG A 471 " model vdw 2.467 2.560 nonbonded pdb=" O GLN A 130 " pdb=" OH TYR A 182 " model vdw 2.471 2.440 ... (remaining 22246 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: 1.890 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: 6.650 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.200 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.012 0.285 2949 Z= 0.785 Angle : 1.267 28.693 4020 Z= 0.827 Chirality : 0.069 0.377 484 Planarity : 0.007 0.062 492 Dihedral : 14.163 89.794 1027 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.67 % Allowed : 17.33 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.40), residues: 382 helix: -1.42 (0.29), residues: 273 sheet: None (None), residues: 0 loop : -2.41 (0.57), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.008 0.001 PHE A 389 TYR 0.019 0.002 TYR A 422 ARG 0.003 0.001 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.238 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 0.1322 time to fit residues: 11.5281 Evaluate side-chains 61 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2949 Z= 0.284 Angle : 0.729 9.719 4020 Z= 0.355 Chirality : 0.044 0.143 484 Planarity : 0.006 0.056 492 Dihedral : 6.562 59.439 422 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.33 % Allowed : 21.33 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.43), residues: 382 helix: 0.16 (0.31), residues: 281 sheet: None (None), residues: 0 loop : -2.23 (0.61), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.011 0.002 PHE A 389 TYR 0.019 0.001 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.274 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 0.1218 time to fit residues: 10.5590 Evaluate side-chains 61 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2949 Z= 0.252 Angle : 0.666 10.365 4020 Z= 0.319 Chirality : 0.042 0.134 484 Planarity : 0.006 0.054 492 Dihedral : 5.993 56.678 420 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.67 % Allowed : 21.67 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.44), residues: 382 helix: 0.53 (0.31), residues: 288 sheet: None (None), residues: 0 loop : -2.06 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.003 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.327 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 0.1167 time to fit residues: 10.3525 Evaluate side-chains 67 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8386 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2949 Z= 0.305 Angle : 0.722 13.607 4020 Z= 0.336 Chirality : 0.043 0.137 484 Planarity : 0.006 0.054 492 Dihedral : 5.084 55.790 416 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.00 % Allowed : 23.67 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.44), residues: 382 helix: 0.65 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -2.01 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.013 0.002 PHE A 238 TYR 0.018 0.002 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.312 Fit side-chains REVERT: A 243 TYR cc_start: 0.8274 (t80) cc_final: 0.7596 (t80) REVERT: A 290 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7665 (mttt) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.1213 time to fit residues: 11.3296 Evaluate side-chains 71 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.0000 chunk 21 optimal weight: 0.9990 overall best weight: 0.3982 ------------------------------------------------------------------------------- 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: 0.8327 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2949 Z= 0.218 Angle : 0.680 13.693 4020 Z= 0.313 Chirality : 0.041 0.118 484 Planarity : 0.006 0.053 492 Dihedral : 4.911 52.436 416 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.33 % Allowed : 23.67 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.44), residues: 382 helix: 0.92 (0.32), residues: 292 sheet: None (None), residues: 0 loop : -2.02 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.001 HIS A 353 PHE 0.023 0.001 PHE A 463 TYR 0.015 0.001 TYR A 422 ARG 0.002 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.272 Fit side-chains REVERT: A 243 TYR cc_start: 0.8271 (t80) cc_final: 0.7507 (t80) REVERT: A 290 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7648 (mttt) outliers start: 16 outliers final: 10 residues processed: 75 average time/residue: 0.1118 time to fit residues: 10.6252 Evaluate side-chains 69 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2949 Z= 0.278 Angle : 0.716 13.972 4020 Z= 0.328 Chirality : 0.042 0.132 484 Planarity : 0.006 0.053 492 Dihedral : 4.922 53.640 416 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.33 % Allowed : 22.33 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.44), residues: 382 helix: 0.96 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -1.84 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.016 0.002 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.282 Fit side-chains REVERT: A 243 TYR cc_start: 0.8266 (t80) cc_final: 0.7514 (t80) REVERT: A 290 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7665 (mttt) REVERT: A 347 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8327 (tt) outliers start: 19 outliers final: 12 residues processed: 79 average time/residue: 0.1157 time to fit residues: 11.4728 Evaluate side-chains 78 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2949 Z= 0.238 Angle : 0.708 13.998 4020 Z= 0.322 Chirality : 0.041 0.121 484 Planarity : 0.006 0.052 492 Dihedral : 4.875 52.238 416 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.67 % Allowed : 24.33 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.44), residues: 382 helix: 1.13 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -1.82 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.016 0.002 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.314 Fit side-chains REVERT: A 243 TYR cc_start: 0.8263 (t80) cc_final: 0.7551 (t80) REVERT: A 290 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7684 (mttt) outliers start: 17 outliers final: 11 residues processed: 73 average time/residue: 0.1226 time to fit residues: 11.3275 Evaluate side-chains 73 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8349 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2949 Z= 0.252 Angle : 0.728 14.215 4020 Z= 0.328 Chirality : 0.042 0.180 484 Planarity : 0.006 0.053 492 Dihedral : 4.841 52.058 416 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.33 % Allowed : 25.00 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.44), residues: 382 helix: 1.19 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -1.82 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.018 0.002 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.296 Fit side-chains REVERT: A 243 TYR cc_start: 0.8237 (t80) cc_final: 0.7524 (t80) REVERT: A 290 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7686 (mttt) outliers start: 16 outliers final: 11 residues processed: 68 average time/residue: 0.1170 time to fit residues: 9.9789 Evaluate side-chains 70 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 0.0050 chunk 22 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 overall best weight: 0.2230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2949 Z= 0.190 Angle : 0.693 14.185 4020 Z= 0.310 Chirality : 0.041 0.158 484 Planarity : 0.006 0.053 492 Dihedral : 4.678 48.445 416 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.33 % Allowed : 27.00 % Favored : 69.67 % 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: 1.08 (0.45), residues: 382 helix: 1.48 (0.32), residues: 290 sheet: None (None), residues: 0 loop : -1.77 (0.60), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.018 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.314 Fit side-chains REVERT: A 243 TYR cc_start: 0.8237 (t80) cc_final: 0.7506 (t80) REVERT: A 290 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7644 (mttt) outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.1259 time to fit residues: 10.2692 Evaluate side-chains 64 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.0000 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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: 0.8322 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2949 Z= 0.240 Angle : 0.727 14.360 4020 Z= 0.324 Chirality : 0.042 0.128 484 Planarity : 0.006 0.053 492 Dihedral : 4.658 49.845 416 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.00 % Allowed : 27.67 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.45), residues: 382 helix: 1.46 (0.32), residues: 290 sheet: None (None), residues: 0 loop : -1.83 (0.60), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.011 0.001 PHE A 463 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.320 Fit side-chains REVERT: A 243 TYR cc_start: 0.8233 (t80) cc_final: 0.7496 (t80) REVERT: A 290 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7683 (mttt) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.1269 time to fit residues: 10.0308 Evaluate side-chains 64 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.0060 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.131513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115591 restraints weight = 4585.939| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.21 r_work: 0.3301 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2949 Z= 0.246 Angle : 0.724 14.389 4020 Z= 0.325 Chirality : 0.042 0.142 484 Planarity : 0.006 0.053 492 Dihedral : 4.720 50.369 416 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.33 % Allowed : 27.00 % Favored : 69.67 % 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: 1.03 (0.44), residues: 382 helix: 1.43 (0.32), residues: 291 sheet: None (None), residues: 0 loop : -1.78 (0.60), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.001 HIS A 353 PHE 0.009 0.001 PHE A 463 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1131.51 seconds wall clock time: 20 minutes 46.68 seconds (1246.68 seconds total)