Starting phenix.real_space_refine on Fri Dec 27 05:43:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jta_36638/12_2024/8jta_36638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jta_36638/12_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/cci-nas-00/data/ceres_data/8jta_36638/12_2024/8jta_36638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jta_36638/12_2024/8jta_36638.map" model { file = "/net/cci-nas-00/data/ceres_data/8jta_36638/12_2024/8jta_36638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jta_36638/12_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. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 2.91, per 1000 atoms: 1.01 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 359.8 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: 0.28 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: 0.76 Time building geometry restraints manager: 0.98 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: 0.00 - 3.61: 3942 3.61 - 7.22: 65 7.22 - 10.83: 9 10.83 - 14.43: 0 14.43 - 18.04: 4 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 3.040 nonbonded pdb=" O PHE A 176 " pdb=" OG SER A 179 " model vdw 2.420 3.040 nonbonded pdb=" O ILE A 194 " pdb=" OG SER A 197 " model vdw 2.459 3.040 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 3.040 ... (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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.660 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.140 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.312 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 0.1320 time to fit residues: 11.5433 Evaluate side-chains 61 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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: 0.6980 chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 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: 0.4858 ------------------------------------------------------------------------------- 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: 0.8312 moved from start: 0.1662 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= 0.235 Angle : 0.710 9.637 4020 Z= 0.345 Chirality : 0.043 0.135 484 Planarity : 0.006 0.056 492 Dihedral : 5.703 50.714 443 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.33 % Allowed : 21.00 % Favored : 74.67 % 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: -0.43 (0.43), residues: 382 helix: 0.39 (0.31), residues: 286 sheet: None (None), residues: 0 loop : -2.20 (0.60), residues: 96 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 0.007 0.001 PHE A 429 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 19 *********************** 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 76 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.282 Fit side-chains REVERT: A 290 LYS cc_start: 0.7984 (mptt) cc_final: 0.7592 (mtpp) outliers start: 13 outliers final: 6 residues processed: 73 average time/residue: 0.1211 time to fit residues: 11.1249 Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 275 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8333 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2949 Z= 0.225 Angle : 0.663 10.113 4020 Z= 0.320 Chirality : 0.041 0.136 484 Planarity : 0.006 0.054 492 Dihedral : 5.384 49.279 443 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.00 % Allowed : 21.67 % Favored : 73.33 % 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: 0.19 (0.44), residues: 382 helix: 0.81 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -2.04 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.014 0.001 PHE A 238 TYR 0.018 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 71 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.319 Fit side-chains REVERT: A 290 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7569 (mtpp) outliers start: 15 outliers final: 7 residues processed: 65 average time/residue: 0.1273 time to fit residues: 10.3330 Evaluate side-chains 60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 270 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 LYS 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: 0.0020 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2949 Z= 0.218 Angle : 0.657 10.253 4020 Z= 0.314 Chirality : 0.041 0.124 484 Planarity : 0.006 0.052 492 Dihedral : 4.420 38.386 439 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.00 % Allowed : 22.00 % Favored : 73.00 % 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: 0.51 (0.44), residues: 382 helix: 1.09 (0.32), residues: 291 sheet: None (None), residues: 0 loop : -2.10 (0.61), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.014 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 *********************** 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 78 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.317 Fit side-chains REVERT: A 243 TYR cc_start: 0.8269 (t80) cc_final: 0.7549 (t80) REVERT: A 290 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7597 (mtpp) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 0.1283 time to fit residues: 11.3991 Evaluate side-chains 69 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 134 LEU 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 405 ILE Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 7 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.2616 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= 0.220 Angle : 0.678 13.288 4020 Z= 0.315 Chirality : 0.041 0.124 484 Planarity : 0.006 0.052 492 Dihedral : 4.384 37.360 439 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.00 % Allowed : 22.33 % 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: 0.70 (0.44), residues: 382 helix: 1.23 (0.32), residues: 291 sheet: None (None), residues: 0 loop : -2.04 (0.61), residues: 91 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 0.024 0.001 PHE A 463 TYR 0.016 0.001 TYR A 422 ARG 0.001 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 77 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.333 Fit side-chains REVERT: A 243 TYR cc_start: 0.8295 (t80) cc_final: 0.7658 (t80) REVERT: A 290 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7591 (mtpp) REVERT: A 443 ILE cc_start: 0.8437 (mm) cc_final: 0.8190 (mt) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 0.1251 time to fit residues: 11.1402 Evaluate side-chains 68 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 270 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 405 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: 1.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8354 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2949 Z= 0.230 Angle : 0.700 13.703 4020 Z= 0.321 Chirality : 0.041 0.124 484 Planarity : 0.006 0.052 492 Dihedral : 4.350 36.775 439 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.33 % Allowed : 21.67 % Favored : 73.00 % 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: 0.87 (0.45), residues: 382 helix: 1.36 (0.32), residues: 291 sheet: None (None), residues: 0 loop : -2.01 (0.60), residues: 91 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 0.015 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.002 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 76 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.320 Fit side-chains REVERT: A 243 TYR cc_start: 0.8299 (t80) cc_final: 0.7690 (t80) REVERT: A 290 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7620 (mtpp) REVERT: A 347 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8278 (tt) REVERT: A 443 ILE cc_start: 0.8452 (mm) cc_final: 0.8238 (mt) REVERT: A 449 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7460 (m-80) outliers start: 16 outliers final: 9 residues processed: 70 average time/residue: 0.1285 time to fit residues: 11.2619 Evaluate side-chains 71 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 449 PHE 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: 0.6980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.0060 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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: 0.2831 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= 0.213 Angle : 0.694 14.007 4020 Z= 0.317 Chirality : 0.041 0.122 484 Planarity : 0.005 0.052 492 Dihedral : 3.971 15.032 437 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.33 % Allowed : 22.00 % 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: 1.04 (0.45), residues: 382 helix: 1.45 (0.32), residues: 292 sheet: None (None), residues: 0 loop : -1.88 (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 0.001 PHE A 238 TYR 0.015 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 77 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.317 Fit side-chains REVERT: A 243 TYR cc_start: 0.8298 (t80) cc_final: 0.7648 (t80) REVERT: A 290 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7607 (mtpp) REVERT: A 347 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8269 (tt) REVERT: A 443 ILE cc_start: 0.8440 (mm) cc_final: 0.8223 (mt) REVERT: A 449 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7431 (m-80) outliers start: 16 outliers final: 11 residues processed: 70 average time/residue: 0.1283 time to fit residues: 11.2242 Evaluate side-chains 74 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 405 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: 1.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.0070 chunk 10 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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: 0.2909 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= 0.214 Angle : 0.710 14.162 4020 Z= 0.321 Chirality : 0.041 0.122 484 Planarity : 0.006 0.052 492 Dihedral : 3.910 14.706 437 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.67 % Allowed : 22.00 % Favored : 72.33 % 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: 1.19 (0.45), residues: 382 helix: 1.55 (0.32), residues: 293 sheet: None (None), residues: 0 loop : -1.81 (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 353 PHE 0.016 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 413 *********************** 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 79 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.323 Fit side-chains REVERT: A 243 TYR cc_start: 0.8303 (t80) cc_final: 0.7734 (t80) REVERT: A 290 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7614 (mtpp) REVERT: A 347 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 389 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: A 443 ILE cc_start: 0.8450 (mm) cc_final: 0.8235 (mt) outliers start: 17 outliers final: 11 residues processed: 73 average time/residue: 0.1343 time to fit residues: 12.3179 Evaluate side-chains 75 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2949 Z= 0.224 Angle : 0.705 14.362 4020 Z= 0.321 Chirality : 0.041 0.123 484 Planarity : 0.006 0.052 492 Dihedral : 3.917 14.716 437 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.33 % Allowed : 23.33 % 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: 1.15 (0.45), residues: 382 helix: 1.48 (0.31), residues: 300 sheet: None (None), residues: 0 loop : -1.92 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.014 0.001 PHE A 449 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 19 *********************** 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 74 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.300 Fit side-chains REVERT: A 243 TYR cc_start: 0.8299 (t80) cc_final: 0.7711 (t80) REVERT: A 290 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7622 (mtpp) REVERT: A 347 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 389 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.7076 (m-80) outliers start: 16 outliers final: 11 residues processed: 67 average time/residue: 0.1253 time to fit residues: 10.4770 Evaluate side-chains 72 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2949 Z= 0.233 Angle : 0.723 14.554 4020 Z= 0.327 Chirality : 0.041 0.123 484 Planarity : 0.006 0.052 492 Dihedral : 3.914 15.012 437 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.33 % Allowed : 24.67 % 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: 1.12 (0.45), residues: 382 helix: 1.46 (0.32), residues: 300 sheet: None (None), residues: 0 loop : -1.94 (0.64), 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 0.016 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 74 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.313 Fit side-chains REVERT: A 169 MET cc_start: 0.7758 (tmm) cc_final: 0.7555 (ttt) REVERT: A 243 TYR cc_start: 0.8325 (t80) cc_final: 0.7714 (t80) REVERT: A 290 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7621 (mtpp) REVERT: A 347 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8251 (tt) REVERT: A 389 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.7081 (m-80) outliers start: 16 outliers final: 11 residues processed: 68 average time/residue: 0.1312 time to fit residues: 11.1894 Evaluate side-chains 72 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.0170 chunk 0 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.132563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116578 restraints weight = 4644.716| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.21 r_work: 0.3310 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3120 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= 0.194 Angle : 0.707 14.310 4020 Z= 0.320 Chirality : 0.041 0.119 484 Planarity : 0.006 0.052 492 Dihedral : 3.859 14.785 437 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.00 % Allowed : 25.33 % 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: 1.26 (0.45), residues: 382 helix: 1.60 (0.32), residues: 297 sheet: None (None), residues: 0 loop : -1.93 (0.62), residues: 85 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 0.010 0.001 PHE A 449 TYR 0.016 0.001 TYR A 382 ARG 0.001 0.000 ARG A 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1106.12 seconds wall clock time: 20 minutes 50.39 seconds (1250.39 seconds total)