Starting phenix.real_space_refine on Thu Jul 18 18:33:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/07_2024/8jta_36638.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/07_2024/8jta_36638.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/07_2024/8jta_36638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/07_2024/8jta_36638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/07_2024/8jta_36638.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jta_36638/07_2024/8jta_36638.cif" } 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-5388/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: 2.65, per 1000 atoms: 0.92 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: 1.10 Conformation dependent library (CDL) restraints added in 652.4 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... Secondary structure from input PDB file: 17 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.507A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 41 through 48 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 128 through 157 removed outlier: 3.552A pdb=" N GLY A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) 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 181 through 211 removed outlier: 3.676A pdb=" N TYR A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 225 through 246 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 249 through 270 removed outlier: 3.720A pdb=" N LEU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) 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 284 through 290 Processing helix chain 'A' and resid 291 through 310 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) Processing helix chain 'A' and resid 334 through 349 removed outlier: 3.607A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) 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) removed outlier: 3.777A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 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 380 through 383 Processing helix chain 'A' and resid 384 through 414 removed outlier: 3.570A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 4.157A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.791A pdb=" N TYR A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) 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 448 through 464 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) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.691A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 561 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: 0.69 Time building geometry restraints manager: 1.18 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 1.504 1.225 0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C8 YHL A 501 " pdb=" C9 YHL A 501 " ideal model delta sigma weight residual 1.517 1.271 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C16 YHL A 501 " pdb=" C17 YHL A 501 " ideal model delta sigma weight residual 1.553 1.349 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C10 YHL A 501 " pdb=" C11 YHL A 501 " ideal model delta sigma weight residual 1.401 1.575 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" C12 YHL A 501 " pdb=" C13 YHL A 501 " ideal model delta sigma weight residual 1.412 1.246 0.166 2.00e-02 2.50e+03 6.89e+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=" 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=" C6 YHL A 501 " pdb=" N7 YHL A 501 " pdb=" C8 YHL A 501 " ideal model delta sigma weight residual 114.81 132.85 -18.04 3.00e+00 1.11e-01 3.62e+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=" C9 YHL A 501 " pdb=" C8 YHL A 501 " pdb=" N7 YHL A 501 " ideal model delta sigma weight residual 109.11 125.95 -16.84 3.00e+00 1.11e-01 3.15e+01 ... (remaining 4015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1567 17.96 - 35.92: 142 35.92 - 53.88: 30 53.88 - 71.84: 4 71.84 - 89.79: 1 Dihedral angle restraints: 1744 sinusoidal: 652 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 1741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 371 0.076 - 0.151: 90 0.151 - 0.226: 18 0.226 - 0.302: 3 0.302 - 0.377: 2 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=" C16 YHL A 501 " pdb=" C15 YHL A 501 " pdb=" C17 YHL A 501 " pdb=" N7 YHL A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.77 0.37 2.00e-01 2.50e+01 3.35e+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 ... (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: 993 2.84 - 3.35: 2988 3.35 - 3.87: 4628 3.87 - 4.38: 5080 4.38 - 4.90: 8514 Nonbonded interactions: 22203 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 22198 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.410 Find NCS groups from input model: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- 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 : 0.013 0.279 2949 Z= 0.807 Angle : 1.264 18.043 4020 Z= 0.827 Chirality : 0.071 0.377 484 Planarity : 0.007 0.062 492 Dihedral : 14.055 89.794 1048 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 : 0.334 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 0.1375 time to fit residues: 11.9912 Evaluate side-chains 61 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8356 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2949 Z= 0.298 Angle : 0.738 9.656 4020 Z= 0.358 Chirality : 0.044 0.145 484 Planarity : 0.006 0.057 492 Dihedral : 5.766 51.402 443 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.00 % Allowed : 20.67 % 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: -0.57 (0.43), residues: 382 helix: 0.30 (0.31), residues: 286 sheet: None (None), residues: 0 loop : -2.29 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.010 0.002 PHE A 429 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 75 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.250 Fit side-chains REVERT: A 290 LYS cc_start: 0.8030 (mptt) cc_final: 0.7620 (mtpp) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 0.1087 time to fit residues: 9.6601 Evaluate side-chains 61 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 134 LEU 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 405 ILE Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.0170 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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: 0.8314 moved from start: 0.2201 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= 0.216 Angle : 0.657 10.604 4020 Z= 0.317 Chirality : 0.041 0.141 484 Planarity : 0.006 0.054 492 Dihedral : 4.760 39.206 441 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: 0.23 (0.44), residues: 382 helix: 0.84 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -2.06 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.013 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.004 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 74 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.317 Fit side-chains REVERT: A 290 LYS cc_start: 0.7943 (mptt) cc_final: 0.7563 (mtpp) REVERT: A 354 LYS cc_start: 0.7890 (tptt) cc_final: 0.7550 (tptp) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.1307 time to fit residues: 10.7977 Evaluate side-chains 68 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 174 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 405 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: 0.2980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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: 0.8364 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2949 Z= 0.269 Angle : 0.693 13.196 4020 Z= 0.324 Chirality : 0.042 0.138 484 Planarity : 0.006 0.053 492 Dihedral : 4.483 38.423 439 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.67 % Allowed : 20.67 % Favored : 72.67 % 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: 0.52 (0.44), residues: 382 helix: 1.07 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -2.01 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.014 0.001 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** 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 79 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.331 Fit side-chains REVERT: A 243 TYR cc_start: 0.8288 (t80) cc_final: 0.7608 (t80) REVERT: A 290 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7649 (mtpp) REVERT: A 443 ILE cc_start: 0.8496 (mm) cc_final: 0.8271 (mt) outliers start: 20 outliers final: 11 residues processed: 72 average time/residue: 0.0968 time to fit residues: 9.0426 Evaluate side-chains 69 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 267 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 405 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: 0.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.8344 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2949 Z= 0.230 Angle : 0.675 13.554 4020 Z= 0.314 Chirality : 0.041 0.129 484 Planarity : 0.006 0.053 492 Dihedral : 4.406 36.979 439 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.67 % Allowed : 22.33 % Favored : 72.00 % 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: 0.79 (0.44), residues: 382 helix: 1.28 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -2.00 (0.61), 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 0.025 0.002 PHE A 463 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** 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: 17 poor density : 63 time to evaluate : 0.257 Fit side-chains REVERT: A 243 TYR cc_start: 0.8318 (t80) cc_final: 0.7653 (t80) REVERT: A 290 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7625 (mtpp) REVERT: A 443 ILE cc_start: 0.8449 (mm) cc_final: 0.8220 (mt) outliers start: 17 outliers final: 11 residues processed: 73 average time/residue: 0.0952 time to fit residues: 8.9361 Evaluate side-chains 71 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 375 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: 2.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2949 Z= 0.229 Angle : 0.686 13.886 4020 Z= 0.316 Chirality : 0.041 0.128 484 Planarity : 0.006 0.053 492 Dihedral : 3.998 17.103 437 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.67 % Allowed : 21.67 % Favored : 71.67 % 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: 1.00 (0.44), residues: 382 helix: 1.44 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -1.94 (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 0.015 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** 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 80 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.288 Fit side-chains REVERT: A 243 TYR cc_start: 0.8299 (t80) cc_final: 0.7681 (t80) REVERT: A 290 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7649 (mtpp) REVERT: A 347 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 389 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: A 443 ILE cc_start: 0.8454 (mm) cc_final: 0.8222 (mt) outliers start: 20 outliers final: 14 residues processed: 72 average time/residue: 0.1028 time to fit residues: 9.5169 Evaluate side-chains 76 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 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 266 GLN Chi-restraints excluded: chain A residue 267 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 311 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 405 ILE 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: 0.9980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2949 Z= 0.251 Angle : 0.694 14.067 4020 Z= 0.321 Chirality : 0.042 0.131 484 Planarity : 0.006 0.052 492 Dihedral : 4.031 17.621 437 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 7.00 % Allowed : 21.33 % Favored : 71.67 % 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: 1.06 (0.44), residues: 382 helix: 1.46 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -1.87 (0.60), residues: 89 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 0.016 0.002 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** 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 81 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 0.337 Fit side-chains REVERT: A 243 TYR cc_start: 0.8317 (t80) cc_final: 0.7749 (t80) REVERT: A 290 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7646 (mtpp) REVERT: A 347 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 389 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: A 449 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7475 (m-80) outliers start: 21 outliers final: 15 residues processed: 72 average time/residue: 0.0934 time to fit residues: 8.7815 Evaluate side-chains 80 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 267 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 311 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 449 PHE 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: 2.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2949 Z= 0.181 Angle : 0.675 14.195 4020 Z= 0.305 Chirality : 0.040 0.117 484 Planarity : 0.005 0.052 492 Dihedral : 3.850 14.913 437 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 6.00 % Allowed : 23.67 % Favored : 70.33 % 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: 1.37 (0.45), residues: 382 helix: 1.70 (0.32), residues: 293 sheet: None (None), residues: 0 loop : -1.85 (0.60), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.001 0.000 HIS A 353 PHE 0.016 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** 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 84 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.333 Fit side-chains REVERT: A 243 TYR cc_start: 0.8295 (t80) cc_final: 0.7713 (t80) REVERT: A 290 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7544 (mtpp) outliers start: 18 outliers final: 12 residues processed: 76 average time/residue: 0.1053 time to fit residues: 10.3088 Evaluate side-chains 74 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 311 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 405 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: 0.9980 chunk 32 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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: 0.8289 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2949 Z= 0.198 Angle : 0.692 14.563 4020 Z= 0.315 Chirality : 0.041 0.180 484 Planarity : 0.005 0.052 492 Dihedral : 3.775 13.882 437 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.00 % Allowed : 24.33 % Favored : 70.67 % 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: 1.36 (0.44), residues: 382 helix: 1.69 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -1.80 (0.60), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.012 0.001 PHE A 449 TYR 0.016 0.001 TYR A 382 ARG 0.001 0.000 ARG A 413 *********************** 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 77 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.324 Fit side-chains REVERT: A 243 TYR cc_start: 0.8299 (t80) cc_final: 0.7704 (t80) REVERT: A 290 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7534 (mtpp) REVERT: A 389 PHE cc_start: 0.7255 (t80) cc_final: 0.7036 (m-80) outliers start: 15 outliers final: 12 residues processed: 71 average time/residue: 0.0932 time to fit residues: 8.6195 Evaluate side-chains 77 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU 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 311 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2949 Z= 0.278 Angle : 0.730 14.753 4020 Z= 0.334 Chirality : 0.043 0.142 484 Planarity : 0.006 0.052 492 Dihedral : 3.932 16.105 437 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.67 % Allowed : 25.33 % 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: 1.13 (0.44), residues: 382 helix: 1.46 (0.31), residues: 300 sheet: None (None), residues: 0 loop : -1.92 (0.62), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.001 0.001 HIS A 353 PHE 0.012 0.001 PHE A 449 TYR 0.021 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 ********************** 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 70 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.318 Fit side-chains REVERT: A 243 TYR cc_start: 0.8331 (t80) cc_final: 0.7705 (t80) REVERT: A 290 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7621 (mtpp) REVERT: A 389 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.7076 (m-80) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1079 time to fit residues: 8.9976 Evaluate side-chains 67 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 267 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 311 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 389 PHE 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: 0.6980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.0040 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.131948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115985 restraints weight = 4631.163| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.20 r_work: 0.3306 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3098 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= 0.229 Angle : 0.705 14.675 4020 Z= 0.322 Chirality : 0.042 0.135 484 Planarity : 0.006 0.052 492 Dihedral : 3.921 15.627 437 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.33 % Allowed : 26.67 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.44), residues: 382 helix: 1.50 (0.31), residues: 300 sheet: None (None), residues: 0 loop : -2.00 (0.62), residues: 82 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 449 TYR 0.016 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: 1080.29 seconds wall clock time: 22 minutes 12.56 seconds (1332.56 seconds total)