Starting phenix.real_space_refine on Tue Mar 11 19:39:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j51_61139/03_2025/9j51_61139.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j51_61139/03_2025/9j51_61139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j51_61139/03_2025/9j51_61139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j51_61139/03_2025/9j51_61139.map" model { file = "/net/cci-nas-00/data/ceres_data/9j51_61139/03_2025/9j51_61139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j51_61139/03_2025/9j51_61139.cif" } resolution = 3.1 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= 0.075 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 30 5.16 5 C 4454 2.51 5 N 1022 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6581 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3174 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 13, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3186 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'PC1': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.82, per 1000 atoms: 0.73 Number of scatterers: 6581 At special positions: 0 Unit cell: (126.26, 67.41, 74.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 5 15.00 O 1070 8.00 N 1022 7.00 C 4454 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 231 through 258 removed outlier: 4.067A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 245 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.237A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.619A pdb=" N PHE A 303 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 345 through 360 removed outlier: 4.486A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.600A pdb=" N THR A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.744A pdb=" N ASN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.278A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.021A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.563A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.505A pdb=" N THR A 545 " --> pdb=" O GLY A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 580 removed outlier: 3.541A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 618 removed outlier: 3.682A pdb=" N ALA A 593 " --> pdb=" O GLY A 589 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.904A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 removed outlier: 3.574A pdb=" N VAL B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 3.874A pdb=" N ILE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 417 removed outlier: 3.656A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.652A pdb=" N ASP B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 502 removed outlier: 3.899A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.532A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 582 removed outlier: 3.953A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 582 " --> pdb=" O SER B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 617 removed outlier: 3.755A pdb=" N ALA B 593 " --> pdb=" O GLY B 589 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.703A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 612 " --> pdb=" O ASN B 608 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 613 " --> pdb=" O PHE B 609 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1263 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: 1.92 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1010 1.32 - 1.45: 2045 1.45 - 1.57: 3682 1.57 - 1.69: 8 1.69 - 1.82: 42 Bond restraints: 6787 Sorted by residual: bond pdb=" C THR A 582 " pdb=" O THR A 582 " ideal model delta sigma weight residual 1.236 1.252 -0.015 7.30e-03 1.88e+04 4.36e+00 bond pdb=" CA ILE B 454 " pdb=" CB ILE B 454 " ideal model delta sigma weight residual 1.539 1.529 0.010 5.40e-03 3.43e+04 3.73e+00 bond pdb=" CA ILE A 360 " pdb=" C ILE A 360 " ideal model delta sigma weight residual 1.524 1.515 0.009 8.60e-03 1.35e+04 1.18e+00 bond pdb=" C ALA A 597 " pdb=" N PRO A 598 " ideal model delta sigma weight residual 1.335 1.348 -0.014 1.28e-02 6.10e+03 1.14e+00 bond pdb=" N ARG B 624 " pdb=" CA ARG B 624 " ideal model delta sigma weight residual 1.458 1.478 -0.020 1.90e-02 2.77e+03 1.14e+00 ... (remaining 6782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 8914 1.37 - 2.74: 222 2.74 - 4.12: 36 4.12 - 5.49: 15 5.49 - 6.86: 2 Bond angle restraints: 9189 Sorted by residual: angle pdb=" C CYS A 453 " pdb=" N ILE A 454 " pdb=" CA ILE A 454 " ideal model delta sigma weight residual 120.33 123.55 -3.22 8.00e-01 1.56e+00 1.62e+01 angle pdb=" C PHE B 623 " pdb=" N ARG B 624 " pdb=" CA ARG B 624 " ideal model delta sigma weight residual 121.70 128.56 -6.86 1.80e+00 3.09e-01 1.45e+01 angle pdb=" CA LEU B 617 " pdb=" C LEU B 617 " pdb=" N ASN B 618 " ideal model delta sigma weight residual 117.79 113.59 4.20 1.22e+00 6.72e-01 1.19e+01 angle pdb=" N GLY B 621 " pdb=" CA GLY B 621 " pdb=" C GLY B 621 " ideal model delta sigma weight residual 114.64 110.11 4.53 1.40e+00 5.10e-01 1.05e+01 angle pdb=" N VAL B 346 " pdb=" CA VAL B 346 " pdb=" C VAL B 346 " ideal model delta sigma weight residual 113.39 109.12 4.27 1.47e+00 4.63e-01 8.44e+00 ... (remaining 9184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3506 17.36 - 34.72: 296 34.72 - 52.08: 81 52.08 - 69.44: 24 69.44 - 86.81: 2 Dihedral angle restraints: 3909 sinusoidal: 1665 harmonic: 2244 Sorted by residual: dihedral pdb=" CA ALA A 384 " pdb=" C ALA A 384 " pdb=" N PRO A 385 " pdb=" CA PRO A 385 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLY A 242 " pdb=" C GLY A 242 " pdb=" N ILE A 243 " pdb=" CA ILE A 243 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASP B 538 " pdb=" CB ASP B 538 " pdb=" CG ASP B 538 " pdb=" OD1 ASP B 538 " ideal model delta sinusoidal sigma weight residual -30.00 -86.01 56.01 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 3906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 533 0.025 - 0.050: 279 0.050 - 0.075: 117 0.075 - 0.100: 39 0.100 - 0.125: 16 Chirality restraints: 984 Sorted by residual: chirality pdb=" CB VAL B 567 " pdb=" CA VAL B 567 " pdb=" CG1 VAL B 567 " pdb=" CG2 VAL B 567 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE A 342 " pdb=" N ILE A 342 " pdb=" C ILE A 342 " pdb=" CB ILE A 342 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA TRP B 266 " pdb=" N TRP B 266 " pdb=" C TRP B 266 " pdb=" CB TRP B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 981 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 242 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C GLY A 242 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY A 242 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 243 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 384 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A 385 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 460 " 0.010 2.00e-02 2.50e+03 9.01e-03 1.42e+00 pdb=" CG PHE A 460 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 460 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 460 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 460 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 460 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 460 " 0.003 2.00e-02 2.50e+03 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 92 2.65 - 3.22: 6358 3.22 - 3.78: 10583 3.78 - 4.34: 14411 4.34 - 4.90: 23475 Nonbonded interactions: 54919 Sorted by model distance: nonbonded pdb=" O LYS A 482 " pdb=" OG1 THR A 485 " model vdw 2.092 3.040 nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.127 3.040 nonbonded pdb=" O LYS B 482 " pdb=" OG1 THR B 485 " model vdw 2.169 3.040 nonbonded pdb=" O GLN A 576 " pdb=" OG1 THR A 580 " model vdw 2.234 3.040 nonbonded pdb=" OG SER A 370 " pdb=" O14 PC1 A 801 " model vdw 2.240 3.040 ... (remaining 54914 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 231 through 624 or resid 801 through 802)) selection = (chain 'B' and (resid 231 through 624 or resid 801 through 802)) } 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: 1.100 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.410 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.003 0.028 6787 Z= 0.206 Angle : 0.547 6.861 9189 Z= 0.314 Chirality : 0.038 0.125 984 Planarity : 0.004 0.051 1095 Dihedral : 14.554 86.805 2461 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.66 % Allowed : 8.12 % Favored : 89.22 % 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: 0.40 (0.31), residues: 754 helix: 1.43 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -3.02 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 607 HIS 0.004 0.001 HIS B 616 PHE 0.021 0.001 PHE A 460 TYR 0.012 0.001 TYR B 518 ARG 0.003 0.000 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8204 (mmm) cc_final: 0.7798 (mmm) REVERT: A 488 PHE cc_start: 0.8141 (m-80) cc_final: 0.7769 (m-80) REVERT: A 504 HIS cc_start: 0.7560 (t-90) cc_final: 0.7239 (t-170) REVERT: A 508 MET cc_start: 0.7767 (mmm) cc_final: 0.7428 (mmm) REVERT: A 511 PHE cc_start: 0.8307 (t80) cc_final: 0.8091 (t80) REVERT: A 528 TRP cc_start: 0.8360 (t-100) cc_final: 0.8116 (t-100) REVERT: B 280 GLU cc_start: 0.8722 (tt0) cc_final: 0.8327 (tt0) REVERT: B 283 PHE cc_start: 0.6853 (t80) cc_final: 0.6561 (t80) REVERT: B 413 MET cc_start: 0.5761 (mtp) cc_final: 0.5446 (mtm) REVERT: B 517 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: B 556 LYS cc_start: 0.7767 (mppt) cc_final: 0.7115 (mtpt) REVERT: B 615 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6903 (tm-30) REVERT: B 624 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.5096 (mmp80) outliers start: 18 outliers final: 8 residues processed: 172 average time/residue: 0.1889 time to fit residues: 42.4502 Evaluate side-chains 134 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 624 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.0000 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 540 ASN B 294 GLN B 387 HIS B 399 GLN B 608 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.186373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158143 restraints weight = 8927.888| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.16 r_work: 0.3682 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6787 Z= 0.209 Angle : 0.552 8.630 9189 Z= 0.296 Chirality : 0.040 0.134 984 Planarity : 0.004 0.049 1095 Dihedral : 11.554 60.497 1050 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.81 % Allowed : 12.11 % Favored : 85.08 % 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: 0.40 (0.31), residues: 754 helix: 1.38 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -2.97 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 607 HIS 0.003 0.001 HIS A 499 PHE 0.022 0.001 PHE B 394 TYR 0.013 0.002 TYR B 518 ARG 0.005 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8219 (mmm) cc_final: 0.7445 (mmm) REVERT: A 488 PHE cc_start: 0.8217 (m-80) cc_final: 0.7756 (m-80) REVERT: A 504 HIS cc_start: 0.7571 (t-90) cc_final: 0.7171 (t-170) REVERT: A 511 PHE cc_start: 0.8328 (t80) cc_final: 0.8070 (t80) REVERT: A 528 TRP cc_start: 0.8399 (t-100) cc_final: 0.8074 (t-100) REVERT: B 283 PHE cc_start: 0.6773 (t80) cc_final: 0.6513 (t80) REVERT: B 409 ASP cc_start: 0.7498 (m-30) cc_final: 0.7176 (m-30) REVERT: B 413 MET cc_start: 0.5563 (mtp) cc_final: 0.5193 (mtp) REVERT: B 517 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7587 (m-10) REVERT: B 556 LYS cc_start: 0.7699 (mppt) cc_final: 0.7021 (mtpt) REVERT: B 615 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6912 (tm-30) outliers start: 19 outliers final: 11 residues processed: 150 average time/residue: 0.1870 time to fit residues: 37.4885 Evaluate side-chains 135 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.184265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155811 restraints weight = 8916.579| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.15 r_work: 0.3659 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6787 Z= 0.240 Angle : 0.565 7.644 9189 Z= 0.297 Chirality : 0.040 0.130 984 Planarity : 0.004 0.053 1095 Dihedral : 11.564 62.176 1040 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.95 % Allowed : 12.70 % Favored : 84.34 % 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: 0.29 (0.31), residues: 754 helix: 1.26 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -2.89 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 607 HIS 0.003 0.001 HIS A 499 PHE 0.024 0.001 PHE B 394 TYR 0.018 0.002 TYR B 290 ARG 0.003 0.000 ARG B 603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 TYR cc_start: 0.8161 (m-80) cc_final: 0.7849 (m-80) REVERT: A 488 PHE cc_start: 0.8235 (m-80) cc_final: 0.7799 (m-80) REVERT: A 504 HIS cc_start: 0.7627 (t-90) cc_final: 0.7339 (t-170) REVERT: A 511 PHE cc_start: 0.8380 (t80) cc_final: 0.8139 (t80) REVERT: A 528 TRP cc_start: 0.8386 (t-100) cc_final: 0.7966 (t-100) REVERT: B 283 PHE cc_start: 0.6841 (t80) cc_final: 0.6481 (t80) REVERT: B 409 ASP cc_start: 0.7585 (m-30) cc_final: 0.7328 (m-30) REVERT: B 413 MET cc_start: 0.5277 (mtp) cc_final: 0.5069 (mtp) REVERT: B 517 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: B 615 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6914 (tm-30) outliers start: 20 outliers final: 14 residues processed: 149 average time/residue: 0.1598 time to fit residues: 32.5588 Evaluate side-chains 133 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 0.3980 chunk 13 optimal weight: 0.0170 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.157684 restraints weight = 9002.955| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.18 r_work: 0.3682 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6787 Z= 0.184 Angle : 0.535 7.203 9189 Z= 0.282 Chirality : 0.040 0.144 984 Planarity : 0.004 0.046 1095 Dihedral : 11.369 61.830 1040 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.25 % Allowed : 13.74 % Favored : 83.01 % 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: 0.50 (0.31), residues: 754 helix: 1.41 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -2.81 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 PHE 0.026 0.001 PHE B 394 TYR 0.018 0.002 TYR A 412 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8213 (m-80) cc_final: 0.7789 (m-80) REVERT: A 496 TYR cc_start: 0.8377 (t80) cc_final: 0.8163 (t80) REVERT: A 504 HIS cc_start: 0.7737 (t-90) cc_final: 0.7395 (t-170) REVERT: A 512 TYR cc_start: 0.8258 (m-10) cc_final: 0.7680 (m-10) REVERT: A 528 TRP cc_start: 0.8390 (t-100) cc_final: 0.8051 (t-100) REVERT: A 532 MET cc_start: 0.6907 (mmt) cc_final: 0.6685 (mmt) REVERT: B 283 PHE cc_start: 0.6757 (t80) cc_final: 0.6496 (t80) REVERT: B 517 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: B 615 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7066 (tm-30) outliers start: 22 outliers final: 18 residues processed: 150 average time/residue: 0.1620 time to fit residues: 33.4461 Evaluate side-chains 146 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.185896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.157492 restraints weight = 8925.431| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.17 r_work: 0.3677 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6787 Z= 0.200 Angle : 0.550 8.448 9189 Z= 0.287 Chirality : 0.041 0.214 984 Planarity : 0.004 0.051 1095 Dihedral : 11.418 61.738 1040 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.25 % Allowed : 14.18 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.31), residues: 754 helix: 1.42 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -2.80 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 PHE 0.027 0.001 PHE B 394 TYR 0.020 0.002 TYR B 290 ARG 0.005 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8223 (m-80) cc_final: 0.7798 (m-80) REVERT: A 500 LYS cc_start: 0.7034 (tttp) cc_final: 0.6778 (ttmm) REVERT: A 504 HIS cc_start: 0.7733 (t-90) cc_final: 0.7380 (t-170) REVERT: A 512 TYR cc_start: 0.8263 (m-10) cc_final: 0.7673 (m-10) REVERT: A 528 TRP cc_start: 0.8387 (t-100) cc_final: 0.7990 (t-100) REVERT: A 532 MET cc_start: 0.6937 (mmt) cc_final: 0.6729 (mmt) REVERT: B 283 PHE cc_start: 0.6798 (t80) cc_final: 0.6422 (t80) REVERT: B 517 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: B 615 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6959 (tm-30) outliers start: 22 outliers final: 18 residues processed: 152 average time/residue: 0.1666 time to fit residues: 34.0551 Evaluate side-chains 144 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 11 optimal weight: 0.0570 chunk 60 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.185366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156839 restraints weight = 8858.448| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.15 r_work: 0.3675 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6787 Z= 0.221 Angle : 0.563 7.575 9189 Z= 0.295 Chirality : 0.041 0.183 984 Planarity : 0.004 0.047 1095 Dihedral : 11.517 62.137 1040 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.40 % Allowed : 14.92 % Favored : 81.68 % 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 (0.31), residues: 754 helix: 1.35 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.72 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 PHE 0.028 0.001 PHE B 394 TYR 0.028 0.002 TYR A 496 ARG 0.006 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 448 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.8008 (mmm-85) REVERT: A 488 PHE cc_start: 0.8227 (m-80) cc_final: 0.7804 (m-80) REVERT: A 512 TYR cc_start: 0.8209 (m-10) cc_final: 0.7648 (m-10) REVERT: A 528 TRP cc_start: 0.8316 (t-100) cc_final: 0.7903 (t-100) REVERT: A 532 MET cc_start: 0.7108 (mmt) cc_final: 0.6897 (mmt) REVERT: B 283 PHE cc_start: 0.6788 (t80) cc_final: 0.6149 (t80) REVERT: B 517 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: B 520 ILE cc_start: 0.6687 (tp) cc_final: 0.6450 (tp) REVERT: B 608 ASN cc_start: 0.8590 (m110) cc_final: 0.8349 (m110) REVERT: B 615 GLU cc_start: 0.7507 (tm-30) cc_final: 0.6976 (tm-30) outliers start: 23 outliers final: 18 residues processed: 151 average time/residue: 0.1850 time to fit residues: 38.1585 Evaluate side-chains 147 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.185810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.157873 restraints weight = 8993.421| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.10 r_work: 0.3689 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6787 Z= 0.205 Angle : 0.556 7.579 9189 Z= 0.291 Chirality : 0.040 0.179 984 Planarity : 0.004 0.051 1095 Dihedral : 11.495 62.278 1040 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.81 % Allowed : 15.95 % Favored : 81.24 % 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 (0.31), residues: 754 helix: 1.40 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.69 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 PHE 0.028 0.001 PHE B 394 TYR 0.022 0.002 TYR A 496 ARG 0.005 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8213 (m-80) cc_final: 0.7821 (m-80) REVERT: A 504 HIS cc_start: 0.7928 (t-90) cc_final: 0.7563 (t-170) REVERT: A 528 TRP cc_start: 0.8301 (t-100) cc_final: 0.7913 (t-100) REVERT: B 283 PHE cc_start: 0.6841 (t80) cc_final: 0.6463 (t80) REVERT: B 517 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: B 608 ASN cc_start: 0.8536 (m110) cc_final: 0.8303 (m110) REVERT: B 615 GLU cc_start: 0.7468 (tm-30) cc_final: 0.6981 (tm-30) outliers start: 19 outliers final: 17 residues processed: 144 average time/residue: 0.1582 time to fit residues: 31.5742 Evaluate side-chains 140 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.185769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157636 restraints weight = 8951.964| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.10 r_work: 0.3687 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6787 Z= 0.207 Angle : 0.561 8.005 9189 Z= 0.294 Chirality : 0.040 0.204 984 Planarity : 0.004 0.046 1095 Dihedral : 11.491 62.671 1039 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.40 % Allowed : 16.54 % Favored : 80.06 % 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: 0.53 (0.31), residues: 754 helix: 1.40 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.65 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 PHE 0.029 0.001 PHE B 394 TYR 0.026 0.002 TYR B 290 ARG 0.006 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8199 (m-80) cc_final: 0.7805 (m-80) REVERT: A 504 HIS cc_start: 0.7897 (t-90) cc_final: 0.7564 (t-170) REVERT: A 528 TRP cc_start: 0.8306 (t-100) cc_final: 0.7875 (t-100) REVERT: B 283 PHE cc_start: 0.6881 (t80) cc_final: 0.6280 (t80) REVERT: B 472 ARG cc_start: 0.7126 (mmm-85) cc_final: 0.5874 (mmp80) REVERT: B 517 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: B 608 ASN cc_start: 0.8518 (m110) cc_final: 0.8309 (m110) REVERT: B 615 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7008 (tm-30) outliers start: 23 outliers final: 19 residues processed: 145 average time/residue: 0.1566 time to fit residues: 31.2321 Evaluate side-chains 141 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 46 optimal weight: 0.0020 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 overall best weight: 0.2188 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.189882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.162110 restraints weight = 8972.515| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.10 r_work: 0.3747 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6787 Z= 0.157 Angle : 0.551 8.079 9189 Z= 0.288 Chirality : 0.040 0.201 984 Planarity : 0.004 0.047 1095 Dihedral : 11.083 60.543 1039 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.81 % Allowed : 17.28 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.32), residues: 754 helix: 1.59 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.62 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 514 HIS 0.002 0.000 HIS A 499 PHE 0.029 0.001 PHE B 394 TYR 0.018 0.001 TYR A 496 ARG 0.005 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8204 (m-80) cc_final: 0.7827 (m-80) REVERT: A 504 HIS cc_start: 0.7710 (t-90) cc_final: 0.7467 (t-170) REVERT: A 508 MET cc_start: 0.7175 (mmm) cc_final: 0.6365 (tpp) REVERT: A 511 PHE cc_start: 0.8192 (t80) cc_final: 0.7839 (t80) REVERT: A 528 TRP cc_start: 0.8261 (t-100) cc_final: 0.7859 (t-100) REVERT: B 283 PHE cc_start: 0.6598 (t80) cc_final: 0.6288 (t80) REVERT: B 472 ARG cc_start: 0.7248 (mmm-85) cc_final: 0.6169 (tpp-160) REVERT: B 517 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: B 520 ILE cc_start: 0.6661 (tp) cc_final: 0.6426 (tp) REVERT: B 608 ASN cc_start: 0.8403 (m110) cc_final: 0.8182 (m110) REVERT: B 615 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6941 (tm-30) outliers start: 19 outliers final: 18 residues processed: 158 average time/residue: 0.1686 time to fit residues: 36.2339 Evaluate side-chains 153 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.187228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.159472 restraints weight = 9101.450| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.11 r_work: 0.3708 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6787 Z= 0.213 Angle : 0.589 7.927 9189 Z= 0.308 Chirality : 0.042 0.259 984 Planarity : 0.004 0.045 1095 Dihedral : 11.196 60.767 1039 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.10 % Allowed : 17.28 % Favored : 79.62 % 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 (0.32), residues: 754 helix: 1.53 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -2.63 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 514 HIS 0.003 0.001 HIS A 499 PHE 0.028 0.001 PHE B 394 TYR 0.026 0.002 TYR B 290 ARG 0.005 0.000 ARG B 472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 PHE cc_start: 0.8228 (m-80) cc_final: 0.7847 (m-80) REVERT: A 528 TRP cc_start: 0.8311 (t-100) cc_final: 0.7960 (t-100) REVERT: B 283 PHE cc_start: 0.6814 (t80) cc_final: 0.6416 (t80) REVERT: B 472 ARG cc_start: 0.7152 (mmm-85) cc_final: 0.6150 (tpp-160) REVERT: B 508 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6235 (ppp) REVERT: B 517 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: B 520 ILE cc_start: 0.6768 (tp) cc_final: 0.6499 (tp) REVERT: B 608 ASN cc_start: 0.8490 (m110) cc_final: 0.8262 (m110) REVERT: B 615 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6900 (tm-30) outliers start: 21 outliers final: 19 residues processed: 142 average time/residue: 0.1542 time to fit residues: 30.4745 Evaluate side-chains 142 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 517 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.187354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.159614 restraints weight = 9016.035| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.10 r_work: 0.3707 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6787 Z= 0.208 Angle : 0.595 8.343 9189 Z= 0.310 Chirality : 0.042 0.247 984 Planarity : 0.004 0.048 1095 Dihedral : 11.240 60.742 1039 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.25 % Allowed : 17.28 % Favored : 79.47 % 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: 0.66 (0.32), residues: 754 helix: 1.49 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -2.64 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 514 HIS 0.002 0.001 HIS A 499 PHE 0.030 0.001 PHE B 394 TYR 0.026 0.002 TYR B 290 ARG 0.005 0.000 ARG B 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.79 seconds wall clock time: 54 minutes 9.86 seconds (3249.86 seconds total)