Starting phenix.real_space_refine on Tue Feb 11 19:26:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrh_37776/02_2025/8wrh_37776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrh_37776/02_2025/8wrh_37776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrh_37776/02_2025/8wrh_37776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrh_37776/02_2025/8wrh_37776.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrh_37776/02_2025/8wrh_37776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrh_37776/02_2025/8wrh_37776.cif" } resolution = 3.08 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= 0.065 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 37 5.16 5 C 4137 2.51 5 N 1069 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6459 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1558 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 14, 'TRANS': 181} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.24, per 1000 atoms: 0.66 Number of scatterers: 6459 At special positions: 0 Unit cell: (71.912, 89.688, 117.16, 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 37 16.00 O 1216 8.00 N 1069 7.00 C 4137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 546 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 53 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 801.8 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 54.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.620A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.568A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.517A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.871A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 Proline residue: A 235 - end of helix removed outlier: 3.794A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.837A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.504A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.672A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.547A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.141A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.570A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.774A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.723A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.655A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.554A pdb=" N PHE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.669A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.537A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.571A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.527A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.757A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.406A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 454 removed outlier: 8.338A pdb=" N ASN B 450 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N SER B 494 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU B 452 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU B 492 " --> pdb=" O LEU B 452 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 858 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: 1.61 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1257 1.33 - 1.45: 1774 1.45 - 1.57: 3555 1.57 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6644 Sorted by residual: bond pdb=" N TYR B 489 " pdb=" CA TYR B 489 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" CA ALA A 80 " pdb=" CB ALA A 80 " ideal model delta sigma weight residual 1.534 1.483 0.050 1.58e-02 4.01e+03 1.02e+01 bond pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.19e-02 7.06e+03 8.06e+00 bond pdb=" CA TYR B 489 " pdb=" C TYR B 489 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.34e-02 5.57e+03 7.11e+00 bond pdb=" N PRO B 486 " pdb=" CA PRO B 486 " ideal model delta sigma weight residual 1.473 1.440 0.033 1.32e-02 5.74e+03 6.22e+00 ... (remaining 6639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 8929 2.62 - 5.24: 87 5.24 - 7.86: 13 7.86 - 10.48: 1 10.48 - 13.10: 1 Bond angle restraints: 9031 Sorted by residual: angle pdb=" N TYR B 489 " pdb=" CA TYR B 489 " pdb=" CB TYR B 489 " ideal model delta sigma weight residual 110.49 123.59 -13.10 1.69e+00 3.50e-01 6.01e+01 angle pdb=" CA PHE B 455 " pdb=" CB PHE B 455 " pdb=" CG PHE B 455 " ideal model delta sigma weight residual 113.80 121.46 -7.66 1.00e+00 1.00e+00 5.87e+01 angle pdb=" N ALA A 80 " pdb=" CA ALA A 80 " pdb=" C ALA A 80 " ideal model delta sigma weight residual 113.50 105.68 7.82 1.23e+00 6.61e-01 4.04e+01 angle pdb=" N LEU A 79 " pdb=" CA LEU A 79 " pdb=" C LEU A 79 " ideal model delta sigma weight residual 113.30 106.59 6.71 1.34e+00 5.57e-01 2.50e+01 angle pdb=" N VAL B 483 " pdb=" CA VAL B 483 " pdb=" C VAL B 483 " ideal model delta sigma weight residual 109.34 119.45 -10.11 2.08e+00 2.31e-01 2.36e+01 ... (remaining 9026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 3457 20.80 - 41.59: 394 41.59 - 62.39: 103 62.39 - 83.18: 13 83.18 - 103.98: 11 Dihedral angle restraints: 3978 sinusoidal: 1658 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 141.28 -48.28 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 44.98 48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 3975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 749 0.050 - 0.099: 164 0.099 - 0.149: 36 0.149 - 0.198: 2 0.198 - 0.248: 3 Chirality restraints: 954 Sorted by residual: chirality pdb=" CA CYS B 488 " pdb=" N CYS B 488 " pdb=" C CYS B 488 " pdb=" CB CYS B 488 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TYR B 489 " pdb=" N TYR B 489 " pdb=" C TYR B 489 " pdb=" CB TYR B 489 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA LEU A 79 " pdb=" N LEU A 79 " pdb=" C LEU A 79 " pdb=" CB LEU A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 951 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 482 " 0.023 2.00e-02 2.50e+03 4.54e-02 2.07e+01 pdb=" C GLY B 482 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY B 482 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL B 483 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 483 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C VAL B 483 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL B 483 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 484 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 455 " 0.019 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE B 455 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 455 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 455 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 455 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 455 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 455 " 0.004 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 172 2.70 - 3.25: 6326 3.25 - 3.80: 10667 3.80 - 4.35: 13447 4.35 - 4.90: 22970 Nonbonded interactions: 53582 Sorted by model distance: nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.151 3.040 nonbonded pdb=" O ASP A 499 " pdb=" OG SER A 502 " model vdw 2.172 3.040 nonbonded pdb=" OE1 GLN A 102 " pdb=" OH TYR A 202 " model vdw 2.193 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.210 3.120 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.216 3.040 ... (remaining 53577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.150 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.680 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.004 0.050 6644 Z= 0.259 Angle : 0.676 13.100 9031 Z= 0.375 Chirality : 0.045 0.248 954 Planarity : 0.004 0.045 1166 Dihedral : 18.702 103.977 2470 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.83 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 24.64 % Favored : 75.36 % Cbeta Deviations : 0.13 % 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: 0.28 (0.30), residues: 786 helix: 1.21 (0.26), residues: 396 sheet: 0.89 (0.81), residues: 44 loop : -1.13 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS A 241 PHE 0.040 0.002 PHE B 455 TYR 0.021 0.002 TYR A 279 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8023 (mtp) cc_final: 0.7782 (mtp) REVERT: A 478 TRP cc_start: 0.6722 (m100) cc_final: 0.6478 (m100) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1408 time to fit residues: 16.9909 Evaluate side-chains 83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.188002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145932 restraints weight = 7265.670| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.58 r_work: 0.3491 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6644 Z= 0.180 Angle : 0.537 7.254 9031 Z= 0.268 Chirality : 0.042 0.185 954 Planarity : 0.004 0.043 1166 Dihedral : 7.150 57.633 940 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 1.44 % Allowed : 22.91 % Favored : 75.65 % 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: 0.44 (0.30), residues: 786 helix: 1.46 (0.26), residues: 396 sheet: 0.96 (0.78), residues: 44 loop : -1.22 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 34 PHE 0.015 0.001 PHE B 455 TYR 0.010 0.001 TYR A 385 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8635 (p) REVERT: A 360 MET cc_start: 0.6761 (ptm) cc_final: 0.6464 (ptm) REVERT: A 364 VAL cc_start: 0.7788 (t) cc_final: 0.7472 (t) REVERT: A 435 GLU cc_start: 0.6779 (pt0) cc_final: 0.6575 (pt0) REVERT: A 544 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.7095 (mt) REVERT: B 500 THR cc_start: 0.8600 (p) cc_final: 0.8354 (p) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 0.1629 time to fit residues: 21.2398 Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.183149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142158 restraints weight = 7385.991| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.23 r_work: 0.3417 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6644 Z= 0.259 Angle : 0.558 7.338 9031 Z= 0.280 Chirality : 0.043 0.156 954 Planarity : 0.004 0.042 1166 Dihedral : 5.139 31.195 940 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.74 % Allowed : 22.19 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.30), residues: 786 helix: 1.52 (0.27), residues: 388 sheet: 0.82 (0.77), residues: 42 loop : -1.17 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 PHE 0.015 0.001 PHE B 455 TYR 0.018 0.002 TYR A 279 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 255 TYR cc_start: 0.7544 (m-80) cc_final: 0.7146 (m-80) REVERT: A 347 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8591 (p) REVERT: A 360 MET cc_start: 0.7201 (ptm) cc_final: 0.6909 (ptm) REVERT: A 364 VAL cc_start: 0.7844 (t) cc_final: 0.7522 (t) REVERT: A 467 GLU cc_start: 0.4243 (OUTLIER) cc_final: 0.3815 (pm20) REVERT: A 544 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7067 (mt) REVERT: B 500 THR cc_start: 0.8625 (p) cc_final: 0.8414 (p) outliers start: 19 outliers final: 11 residues processed: 101 average time/residue: 0.1631 time to fit residues: 23.0865 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.181495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140776 restraints weight = 7401.654| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.13 r_work: 0.3425 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6644 Z= 0.261 Angle : 0.557 7.490 9031 Z= 0.280 Chirality : 0.043 0.145 954 Planarity : 0.004 0.043 1166 Dihedral : 4.781 27.297 940 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.89 % Allowed : 20.46 % Favored : 75.65 % 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: 0.32 (0.30), residues: 786 helix: 1.27 (0.26), residues: 403 sheet: 0.66 (0.75), residues: 42 loop : -1.15 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.014 0.001 PHE B 455 TYR 0.020 0.002 TYR A 279 ARG 0.006 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.8078 (mtp) cc_final: 0.7852 (mtp) REVERT: A 83 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: A 259 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6578 (pt) REVERT: A 347 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 360 MET cc_start: 0.7327 (ptm) cc_final: 0.7041 (ptm) REVERT: A 364 VAL cc_start: 0.8026 (t) cc_final: 0.7745 (t) REVERT: A 383 MET cc_start: 0.9363 (mtp) cc_final: 0.9124 (mtm) REVERT: A 467 GLU cc_start: 0.4632 (OUTLIER) cc_final: 0.3305 (pt0) REVERT: A 470 LYS cc_start: 0.7732 (tttm) cc_final: 0.7491 (ttpp) REVERT: A 544 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7224 (mt) REVERT: B 466 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.4885 (ttm170) REVERT: B 500 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8402 (p) outliers start: 27 outliers final: 12 residues processed: 105 average time/residue: 0.1696 time to fit residues: 24.6911 Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.180216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140413 restraints weight = 7341.161| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.09 r_work: 0.3424 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6644 Z= 0.224 Angle : 0.540 7.509 9031 Z= 0.269 Chirality : 0.042 0.138 954 Planarity : 0.004 0.043 1166 Dihedral : 4.561 25.456 940 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.59 % Allowed : 22.48 % Favored : 74.93 % 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: 0.38 (0.30), residues: 786 helix: 1.39 (0.26), residues: 396 sheet: 0.55 (0.75), residues: 42 loop : -1.15 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 34 PHE 0.012 0.001 PHE B 455 TYR 0.014 0.001 TYR A 385 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: A 166 GLU cc_start: 0.7660 (tp30) cc_final: 0.6735 (tp30) REVERT: A 347 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8586 (p) REVERT: A 360 MET cc_start: 0.7288 (ptm) cc_final: 0.7016 (ptm) REVERT: A 364 VAL cc_start: 0.7970 (t) cc_final: 0.7705 (t) REVERT: A 544 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7146 (mt) REVERT: B 478 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6824 (mtpp) REVERT: B 500 THR cc_start: 0.8578 (p) cc_final: 0.8294 (p) outliers start: 18 outliers final: 12 residues processed: 101 average time/residue: 0.1647 time to fit residues: 23.3129 Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.183311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142037 restraints weight = 7284.436| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.19 r_work: 0.3440 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6644 Z= 0.177 Angle : 0.510 7.345 9031 Z= 0.253 Chirality : 0.041 0.136 954 Planarity : 0.004 0.043 1166 Dihedral : 4.291 24.378 940 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.74 % Allowed : 23.78 % Favored : 73.49 % 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 (0.30), residues: 786 helix: 1.63 (0.27), residues: 390 sheet: 0.65 (0.76), residues: 44 loop : -1.23 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE B 455 TYR 0.020 0.001 TYR A 279 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.701 Fit side-chains REVERT: A 166 GLU cc_start: 0.7564 (tp30) cc_final: 0.6677 (tp30) REVERT: A 259 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6664 (pt) REVERT: A 347 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8612 (p) REVERT: A 364 VAL cc_start: 0.7978 (t) cc_final: 0.7702 (t) REVERT: A 467 GLU cc_start: 0.4343 (OUTLIER) cc_final: 0.3363 (pt0) REVERT: A 544 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7135 (mt) REVERT: B 466 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.4653 (ttm170) REVERT: B 478 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6741 (mtpp) REVERT: B 500 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8220 (p) outliers start: 19 outliers final: 10 residues processed: 102 average time/residue: 0.1657 time to fit residues: 23.3669 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 70 optimal weight: 0.0070 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.184881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143862 restraints weight = 7325.617| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.24 r_work: 0.3448 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6644 Z= 0.153 Angle : 0.498 7.259 9031 Z= 0.248 Chirality : 0.041 0.160 954 Planarity : 0.003 0.044 1166 Dihedral : 3.985 22.727 940 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.16 % Allowed : 23.78 % Favored : 74.06 % 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: 0.63 (0.30), residues: 786 helix: 1.75 (0.27), residues: 390 sheet: 0.67 (0.76), residues: 44 loop : -1.20 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.002 0.001 HIS A 34 PHE 0.010 0.001 PHE A 327 TYR 0.020 0.001 TYR A 279 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.693 Fit side-chains REVERT: A 166 GLU cc_start: 0.7530 (tp30) cc_final: 0.6655 (tp30) REVERT: A 279 TYR cc_start: 0.7085 (t80) cc_final: 0.6843 (t80) REVERT: A 347 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8591 (p) REVERT: A 360 MET cc_start: 0.6647 (ptm) cc_final: 0.6350 (ptm) REVERT: A 364 VAL cc_start: 0.7989 (t) cc_final: 0.7708 (t) REVERT: A 467 GLU cc_start: 0.4397 (OUTLIER) cc_final: 0.3450 (pt0) REVERT: A 544 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7115 (mt) REVERT: B 466 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.4503 (ttm170) REVERT: B 478 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6622 (mtpp) REVERT: B 500 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8189 (p) outliers start: 15 outliers final: 7 residues processed: 103 average time/residue: 0.1655 time to fit residues: 23.6339 Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.182206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141774 restraints weight = 7325.162| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.11 r_work: 0.3422 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6644 Z= 0.219 Angle : 0.528 7.421 9031 Z= 0.266 Chirality : 0.042 0.149 954 Planarity : 0.004 0.044 1166 Dihedral : 4.119 23.317 940 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.45 % Allowed : 23.92 % Favored : 73.63 % 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: 0.68 (0.30), residues: 786 helix: 1.88 (0.27), residues: 378 sheet: -0.07 (0.69), residues: 52 loop : -1.08 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.018 0.001 PHE B 455 TYR 0.019 0.001 TYR A 279 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.688 Fit side-chains REVERT: A 166 GLU cc_start: 0.7576 (tp30) cc_final: 0.6704 (tp30) REVERT: A 347 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 360 MET cc_start: 0.7064 (ptm) cc_final: 0.6737 (ptm) REVERT: A 467 GLU cc_start: 0.4433 (OUTLIER) cc_final: 0.3509 (pt0) REVERT: A 544 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7140 (mt) REVERT: B 466 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.4767 (ttm170) REVERT: B 478 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6879 (mtpp) REVERT: B 500 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8317 (p) REVERT: B 508 TYR cc_start: 0.8882 (m-80) cc_final: 0.8658 (m-80) outliers start: 17 outliers final: 9 residues processed: 105 average time/residue: 0.1668 time to fit residues: 24.3603 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.181009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140613 restraints weight = 7424.622| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.14 r_work: 0.3409 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6644 Z= 0.236 Angle : 0.539 7.339 9031 Z= 0.271 Chirality : 0.042 0.155 954 Planarity : 0.004 0.044 1166 Dihedral : 4.239 23.588 940 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.45 % Allowed : 24.21 % Favored : 73.34 % 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: 0.59 (0.30), residues: 786 helix: 1.75 (0.27), residues: 382 sheet: 0.53 (0.74), residues: 42 loop : -1.16 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.004 0.001 HIS A 241 PHE 0.016 0.001 PHE B 455 TYR 0.022 0.001 TYR A 279 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8586 (p) REVERT: A 360 MET cc_start: 0.7132 (ptm) cc_final: 0.6802 (ptm) REVERT: A 467 GLU cc_start: 0.4429 (OUTLIER) cc_final: 0.3564 (pt0) REVERT: A 544 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7147 (mt) REVERT: B 466 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.4737 (ttm170) REVERT: B 478 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6573 (mtpp) REVERT: B 500 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8330 (p) outliers start: 17 outliers final: 10 residues processed: 102 average time/residue: 0.1666 time to fit residues: 23.5179 Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.0170 chunk 9 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 0.0770 chunk 36 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.185171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145542 restraints weight = 7327.877| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.10 r_work: 0.3457 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6644 Z= 0.154 Angle : 0.507 7.319 9031 Z= 0.254 Chirality : 0.041 0.141 954 Planarity : 0.003 0.044 1166 Dihedral : 3.942 21.590 940 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.44 % Allowed : 25.07 % Favored : 73.49 % 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 (0.30), residues: 786 helix: 1.89 (0.27), residues: 382 sheet: -0.04 (0.71), residues: 54 loop : -1.10 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 PHE 0.011 0.001 PHE B 455 TYR 0.021 0.001 TYR A 279 ARG 0.003 0.000 ARG A 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.692 Fit side-chains REVERT: A 279 TYR cc_start: 0.7087 (t80) cc_final: 0.6869 (t80) REVERT: A 347 THR cc_start: 0.8935 (p) cc_final: 0.8616 (p) REVERT: A 510 TYR cc_start: 0.8371 (m-80) cc_final: 0.8107 (m-80) REVERT: B 466 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.4539 (ttm170) REVERT: B 500 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8228 (p) REVERT: B 508 TYR cc_start: 0.8844 (m-80) cc_final: 0.8614 (m-80) outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.1615 time to fit residues: 22.2680 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.182484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142944 restraints weight = 7468.248| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.11 r_work: 0.3429 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6644 Z= 0.197 Angle : 0.530 7.473 9031 Z= 0.266 Chirality : 0.041 0.141 954 Planarity : 0.004 0.044 1166 Dihedral : 4.010 21.663 940 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.73 % Allowed : 24.78 % Favored : 73.49 % 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: 0.69 (0.30), residues: 786 helix: 1.87 (0.27), residues: 382 sheet: -0.06 (0.70), residues: 52 loop : -1.09 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 168 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 327 TYR 0.022 0.001 TYR A 279 ARG 0.003 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.33 seconds wall clock time: 60 minutes 15.92 seconds (3615.92 seconds total)