Starting phenix.real_space_refine on Tue Jan 14 11:41:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yfx_39232/01_2025/8yfx_39232.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yfx_39232/01_2025/8yfx_39232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yfx_39232/01_2025/8yfx_39232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yfx_39232/01_2025/8yfx_39232.map" model { file = "/net/cci-nas-00/data/ceres_data/8yfx_39232/01_2025/8yfx_39232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yfx_39232/01_2025/8yfx_39232.cif" } resolution = 3.56 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= 0.088 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 32 5.16 5 C 4414 2.51 5 N 1054 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3294 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain: "B" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3294 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Time building chain proxies: 4.42, per 1000 atoms: 0.67 Number of scatterers: 6588 At special positions: 0 Unit cell: (79.2, 68.2, 130.9, 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 32 16.00 O 1088 8.00 N 1054 7.00 C 4414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 966.1 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.711A pdb=" N THR A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 5.052A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.985A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 removed outlier: 3.737A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.603A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.969A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 removed outlier: 4.128A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.397A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.773A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A 527 " --> pdb=" O CYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 583 removed outlier: 3.884A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 622 removed outlier: 4.599A pdb=" N ILE A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 4.241A pdb=" N VAL A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 602 " --> pdb=" O PRO A 598 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 removed outlier: 3.678A pdb=" N THR B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.955A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.754A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.175A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 503 removed outlier: 4.063A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.775A pdb=" N TYR B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 527 " --> pdb=" O CYS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 583 removed outlier: 4.325A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 581 " --> pdb=" O ILE B 577 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 622 Proline residue: B 598 - end of helix removed outlier: 4.289A pdb=" N VAL B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE B 602 " --> pdb=" O PRO B 598 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1326 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: 1.79 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1922 1.34 - 1.46: 1431 1.46 - 1.58: 3411 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 6808 Sorted by residual: bond pdb=" CA TYR A 368 " pdb=" C TYR A 368 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.34e-02 5.57e+03 2.56e+00 bond pdb=" CB LYS A 369 " pdb=" CG LYS A 369 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.82e+00 bond pdb=" C ALA A 384 " pdb=" N PRO A 385 " ideal model delta sigma weight residual 1.337 1.347 -0.011 9.80e-03 1.04e+04 1.16e+00 bond pdb=" CB TYR A 496 " pdb=" CG TYR A 496 " ideal model delta sigma weight residual 1.512 1.535 -0.023 2.20e-02 2.07e+03 1.08e+00 bond pdb=" CB ASN A 288 " pdb=" CG ASN A 288 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.96e-01 ... (remaining 6803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 8944 1.53 - 3.07: 269 3.07 - 4.60: 34 4.60 - 6.14: 16 6.14 - 7.67: 5 Bond angle restraints: 9268 Sorted by residual: angle pdb=" CA LYS A 471 " pdb=" CB LYS A 471 " pdb=" CG LYS A 471 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 111.58 107.91 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" CA GLU A 304 " pdb=" CB GLU A 304 " pdb=" CG GLU A 304 " ideal model delta sigma weight residual 114.10 121.00 -6.90 2.00e+00 2.50e-01 1.19e+01 angle pdb=" N ALA B 473 " pdb=" CA ALA B 473 " pdb=" C ALA B 473 " ideal model delta sigma weight residual 110.97 114.53 -3.56 1.09e+00 8.42e-01 1.07e+01 angle pdb=" C VAL B 595 " pdb=" N PHE B 596 " pdb=" CA PHE B 596 " ideal model delta sigma weight residual 122.65 117.84 4.81 1.60e+00 3.91e-01 9.02e+00 ... (remaining 9263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 3275 17.03 - 34.07: 444 34.07 - 51.10: 131 51.10 - 68.14: 10 68.14 - 85.17: 8 Dihedral angle restraints: 3868 sinusoidal: 1532 harmonic: 2336 Sorted by residual: dihedral pdb=" CA ALA B 473 " pdb=" C ALA B 473 " pdb=" N PHE B 474 " pdb=" CA PHE B 474 " ideal model delta harmonic sigma weight residual -180.00 -158.99 -21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ILE B 342 " pdb=" C ILE B 342 " pdb=" N PRO B 343 " pdb=" CA PRO B 343 " ideal model delta harmonic sigma weight residual -180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE A 511 " pdb=" C PHE A 511 " pdb=" N TYR A 512 " pdb=" CA TYR A 512 " ideal model delta harmonic sigma weight residual -180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 3865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 666 0.039 - 0.078: 267 0.078 - 0.117: 66 0.117 - 0.156: 9 0.156 - 0.195: 4 Chirality restraints: 1012 Sorted by residual: chirality pdb=" CG LEU B 617 " pdb=" CB LEU B 617 " pdb=" CD1 LEU B 617 " pdb=" CD2 LEU B 617 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CB VAL B 595 " pdb=" CA VAL B 595 " pdb=" CG1 VAL B 595 " pdb=" CG2 VAL B 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA PHE B 596 " pdb=" N PHE B 596 " pdb=" C PHE B 596 " pdb=" CB PHE B 596 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 1009 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 496 " 0.007 2.00e-02 2.50e+03 1.98e-02 7.82e+00 pdb=" CG TYR A 496 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 496 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 496 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 496 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 496 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 496 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 496 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 304 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C GLU A 304 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU A 304 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 305 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 430 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 431 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " -0.022 5.00e-02 4.00e+02 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 63 2.64 - 3.20: 6282 3.20 - 3.77: 10327 3.77 - 4.33: 12774 4.33 - 4.90: 21442 Nonbonded interactions: 50888 Sorted by model distance: nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.071 3.040 nonbonded pdb=" O ARG A 466 " pdb=" OG1 THR A 470 " model vdw 2.149 3.040 nonbonded pdb=" OD1 ASP A 533 " pdb=" NH1 ARG A 611 " model vdw 2.151 3.120 nonbonded pdb=" NH2 ARG B 548 " pdb=" OE2 GLU B 613 " model vdw 2.164 3.120 nonbonded pdb=" O SER A 578 " pdb=" OG1 THR A 582 " model vdw 2.181 3.040 ... (remaining 50883 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.790 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.300 Find NCS groups from input model: 0.180 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 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 0.040 6808 Z= 0.257 Angle : 0.648 7.670 9268 Z= 0.364 Chirality : 0.045 0.195 1012 Planarity : 0.005 0.040 1134 Dihedral : 16.588 85.173 2358 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.28 % Allowed : 21.31 % Favored : 78.41 % 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: 0.74 (0.31), residues: 788 helix: 1.56 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -2.08 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 266 HIS 0.007 0.001 HIS A 313 PHE 0.024 0.002 PHE B 596 TYR 0.043 0.002 TYR A 496 ARG 0.003 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.755 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 103 average time/residue: 0.1879 time to fit residues: 26.0052 Evaluate side-chains 98 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN ** B 306 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 = 0.4346 r_free = 0.4346 target = 0.209868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.172315 restraints weight = 7964.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.175804 restraints weight = 5335.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.178176 restraints weight = 4204.264| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6808 Z= 0.185 Angle : 0.557 6.073 9268 Z= 0.303 Chirality : 0.041 0.144 1012 Planarity : 0.004 0.039 1134 Dihedral : 4.749 49.529 876 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.12 % Allowed : 19.18 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.31), residues: 788 helix: 1.92 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -2.08 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 266 HIS 0.006 0.001 HIS A 504 PHE 0.023 0.001 PHE B 596 TYR 0.017 0.002 TYR B 558 ARG 0.004 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.757 Fit side-chains REVERT: A 483 TYR cc_start: 0.7503 (m-80) cc_final: 0.7189 (m-80) REVERT: A 496 TYR cc_start: 0.5877 (t80) cc_final: 0.5569 (t80) REVERT: A 508 MET cc_start: 0.7276 (pmm) cc_final: 0.7022 (ttt) REVERT: B 617 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8406 (mm) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 0.1749 time to fit residues: 28.9174 Evaluate side-chains 109 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.207825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.169100 restraints weight = 8101.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173096 restraints weight = 5184.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.175704 restraints weight = 3966.547| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6808 Z= 0.209 Angle : 0.554 5.986 9268 Z= 0.299 Chirality : 0.042 0.156 1012 Planarity : 0.004 0.033 1134 Dihedral : 4.665 52.086 874 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.84 % Allowed : 19.89 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.30), residues: 788 helix: 2.02 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -2.09 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 266 HIS 0.006 0.001 HIS A 313 PHE 0.025 0.001 PHE B 596 TYR 0.019 0.002 TYR B 558 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.664 Fit side-chains REVERT: A 394 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.6999 (p90) REVERT: A 457 TRP cc_start: 0.7842 (t-100) cc_final: 0.7487 (t-100) REVERT: A 483 TYR cc_start: 0.7609 (m-80) cc_final: 0.7178 (m-80) REVERT: A 570 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6933 (mmt-90) outliers start: 27 outliers final: 16 residues processed: 129 average time/residue: 0.1760 time to fit residues: 30.7500 Evaluate side-chains 114 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.0570 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 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 = 0.4327 r_free = 0.4327 target = 0.207897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.168336 restraints weight = 8258.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.172299 restraints weight = 5379.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.174912 restraints weight = 4149.357| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6808 Z= 0.189 Angle : 0.550 9.351 9268 Z= 0.294 Chirality : 0.041 0.163 1012 Planarity : 0.004 0.036 1134 Dihedral : 4.637 54.179 874 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.98 % Allowed : 21.02 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.31), residues: 788 helix: 2.15 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -1.99 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 292 HIS 0.006 0.001 HIS A 504 PHE 0.031 0.001 PHE B 596 TYR 0.019 0.001 TYR B 558 ARG 0.003 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.709 Fit side-chains REVERT: A 394 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7034 (p90) REVERT: A 483 TYR cc_start: 0.7570 (m-80) cc_final: 0.7111 (m-80) REVERT: A 515 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.7956 (mm) REVERT: A 570 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6942 (mmt-90) outliers start: 28 outliers final: 17 residues processed: 128 average time/residue: 0.1639 time to fit residues: 29.0896 Evaluate side-chains 120 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 52 optimal weight: 0.0040 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN B 587 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.208038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.168746 restraints weight = 8206.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.172710 restraints weight = 5352.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.175252 restraints weight = 4158.346| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6808 Z= 0.188 Angle : 0.544 7.572 9268 Z= 0.293 Chirality : 0.042 0.169 1012 Planarity : 0.004 0.036 1134 Dihedral : 4.643 56.817 874 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.11 % Allowed : 20.60 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.31), residues: 788 helix: 2.14 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.97 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 292 HIS 0.005 0.001 HIS A 504 PHE 0.028 0.001 PHE B 596 TYR 0.019 0.001 TYR B 558 ARG 0.003 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.679 Fit side-chains REVERT: A 408 MET cc_start: 0.7584 (tpp) cc_final: 0.7295 (tpp) REVERT: A 483 TYR cc_start: 0.7644 (m-80) cc_final: 0.7140 (m-80) REVERT: A 570 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6937 (mmt-90) REVERT: B 270 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7505 (ttm-80) outliers start: 36 outliers final: 21 residues processed: 142 average time/residue: 0.1699 time to fit residues: 32.6903 Evaluate side-chains 126 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 590 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 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 = 0.4325 r_free = 0.4325 target = 0.207646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.168714 restraints weight = 8048.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.172507 restraints weight = 5251.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175043 restraints weight = 4076.349| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6808 Z= 0.206 Angle : 0.562 7.299 9268 Z= 0.303 Chirality : 0.042 0.176 1012 Planarity : 0.004 0.049 1134 Dihedral : 4.694 59.987 874 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.69 % Allowed : 22.16 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.31), residues: 788 helix: 2.13 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.94 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 292 HIS 0.005 0.001 HIS A 504 PHE 0.029 0.001 PHE B 596 TYR 0.019 0.002 TYR B 558 ARG 0.004 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.685 Fit side-chains REVERT: A 408 MET cc_start: 0.7566 (tpp) cc_final: 0.7276 (tpp) REVERT: A 419 LEU cc_start: 0.8240 (tt) cc_final: 0.8015 (mm) REVERT: A 483 TYR cc_start: 0.7708 (m-80) cc_final: 0.7226 (m-80) REVERT: A 570 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6871 (mmt-90) REVERT: B 270 ARG cc_start: 0.7726 (tpp80) cc_final: 0.7506 (ttm-80) outliers start: 33 outliers final: 18 residues processed: 137 average time/residue: 0.1615 time to fit residues: 30.0630 Evaluate side-chains 124 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.0020 chunk 51 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 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 = 0.4327 r_free = 0.4327 target = 0.207460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.168043 restraints weight = 8196.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.171950 restraints weight = 5347.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174487 restraints weight = 4152.981| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6808 Z= 0.181 Angle : 0.556 8.009 9268 Z= 0.299 Chirality : 0.042 0.223 1012 Planarity : 0.004 0.036 1134 Dihedral : 4.644 57.524 874 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.12 % Allowed : 22.59 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.31), residues: 788 helix: 2.24 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -1.85 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 292 HIS 0.005 0.001 HIS A 504 PHE 0.020 0.001 PHE B 596 TYR 0.020 0.001 TYR B 518 ARG 0.003 0.000 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.738 Fit side-chains REVERT: A 408 MET cc_start: 0.7652 (tpp) cc_final: 0.7327 (tpp) REVERT: A 419 LEU cc_start: 0.8281 (tt) cc_final: 0.8048 (mm) REVERT: A 483 TYR cc_start: 0.7723 (m-80) cc_final: 0.7243 (m-80) REVERT: A 570 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6852 (mmt-90) REVERT: B 293 ARG cc_start: 0.6530 (tpm170) cc_final: 0.5522 (tpp-160) REVERT: B 607 TRP cc_start: 0.6823 (t60) cc_final: 0.6421 (t60) outliers start: 29 outliers final: 21 residues processed: 133 average time/residue: 0.1576 time to fit residues: 28.8959 Evaluate side-chains 125 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 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 = 0.4329 r_free = 0.4329 target = 0.207951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.168720 restraints weight = 8208.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172702 restraints weight = 5334.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.174820 restraints weight = 4126.984| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6808 Z= 0.183 Angle : 0.556 8.243 9268 Z= 0.301 Chirality : 0.042 0.215 1012 Planarity : 0.004 0.035 1134 Dihedral : 4.615 55.579 874 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.98 % Allowed : 23.15 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.31), residues: 788 helix: 2.24 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -1.86 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 292 HIS 0.005 0.001 HIS A 504 PHE 0.016 0.001 PHE B 596 TYR 0.019 0.001 TYR B 518 ARG 0.004 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.674 Fit side-chains REVERT: A 408 MET cc_start: 0.7665 (tpp) cc_final: 0.7318 (tpp) REVERT: A 419 LEU cc_start: 0.8325 (tt) cc_final: 0.8101 (mm) REVERT: A 448 ARG cc_start: 0.7137 (mpp-170) cc_final: 0.6901 (mtm-85) REVERT: A 457 TRP cc_start: 0.7845 (t-100) cc_final: 0.7568 (t-100) REVERT: A 483 TYR cc_start: 0.7683 (m-80) cc_final: 0.7153 (m-80) REVERT: A 570 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6839 (mmt-90) REVERT: A 611 ARG cc_start: 0.8016 (tpt-90) cc_final: 0.7460 (tpt170) REVERT: B 292 TRP cc_start: 0.7509 (m-90) cc_final: 0.6627 (m-90) REVERT: B 607 TRP cc_start: 0.6792 (t60) cc_final: 0.6383 (t60) outliers start: 28 outliers final: 21 residues processed: 134 average time/residue: 0.1781 time to fit residues: 33.0895 Evaluate side-chains 131 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** B 306 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 = 0.4340 r_free = 0.4340 target = 0.208960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.169923 restraints weight = 8184.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.173745 restraints weight = 5314.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.175990 restraints weight = 4111.714| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6808 Z= 0.180 Angle : 0.556 8.488 9268 Z= 0.301 Chirality : 0.042 0.212 1012 Planarity : 0.004 0.034 1134 Dihedral : 4.574 53.901 874 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.55 % Allowed : 23.58 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.31), residues: 788 helix: 2.27 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.86 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 292 HIS 0.006 0.001 HIS A 504 PHE 0.016 0.001 PHE B 596 TYR 0.019 0.001 TYR B 518 ARG 0.002 0.000 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.690 Fit side-chains REVERT: A 408 MET cc_start: 0.7664 (tpp) cc_final: 0.7322 (tpp) REVERT: A 419 LEU cc_start: 0.8315 (tt) cc_final: 0.8102 (mm) REVERT: A 483 TYR cc_start: 0.7638 (m-80) cc_final: 0.7041 (m-80) REVERT: A 570 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6915 (mmt-90) REVERT: A 611 ARG cc_start: 0.7906 (tpt-90) cc_final: 0.7465 (tpt170) REVERT: B 322 PHE cc_start: 0.7198 (t80) cc_final: 0.6975 (t80) REVERT: B 607 TRP cc_start: 0.6829 (t60) cc_final: 0.6416 (t60) outliers start: 25 outliers final: 20 residues processed: 129 average time/residue: 0.1725 time to fit residues: 30.3096 Evaluate side-chains 127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 0.0570 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 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 = 0.4337 r_free = 0.4337 target = 0.208578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.169361 restraints weight = 8195.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173324 restraints weight = 5318.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175926 restraints weight = 4106.784| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6808 Z= 0.191 Angle : 0.584 8.588 9268 Z= 0.312 Chirality : 0.042 0.260 1012 Planarity : 0.004 0.034 1134 Dihedral : 4.524 52.906 874 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.98 % Allowed : 24.15 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.31), residues: 788 helix: 2.23 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.83 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 292 HIS 0.003 0.001 HIS A 313 PHE 0.018 0.001 PHE B 596 TYR 0.019 0.002 TYR B 518 ARG 0.005 0.000 ARG A 448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.7681 (tpp) cc_final: 0.7345 (tpp) REVERT: A 419 LEU cc_start: 0.8307 (tt) cc_final: 0.8097 (mm) REVERT: A 457 TRP cc_start: 0.7813 (t-100) cc_final: 0.7549 (t-100) REVERT: A 483 TYR cc_start: 0.7607 (m-80) cc_final: 0.7003 (m-80) REVERT: A 570 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6928 (mmt-90) REVERT: A 611 ARG cc_start: 0.7858 (tpt-90) cc_final: 0.7447 (tpt170) REVERT: B 292 TRP cc_start: 0.7487 (m-90) cc_final: 0.6713 (m-90) REVERT: B 607 TRP cc_start: 0.6775 (t60) cc_final: 0.6375 (t60) outliers start: 21 outliers final: 19 residues processed: 124 average time/residue: 0.1688 time to fit residues: 28.5147 Evaluate side-chains 126 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 423 TRP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 0.0070 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** B 306 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 = 0.4333 r_free = 0.4333 target = 0.207996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.168662 restraints weight = 8291.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.172700 restraints weight = 5359.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.175333 restraints weight = 4120.760| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6808 Z= 0.199 Angle : 0.584 8.479 9268 Z= 0.312 Chirality : 0.042 0.231 1012 Planarity : 0.004 0.033 1134 Dihedral : 4.542 51.368 874 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.98 % Allowed : 24.29 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.31), residues: 788 helix: 2.20 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.82 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 292 HIS 0.007 0.001 HIS A 504 PHE 0.021 0.001 PHE B 322 TYR 0.016 0.002 TYR B 345 ARG 0.005 0.000 ARG A 448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.77 seconds wall clock time: 38 minutes 30.17 seconds (2310.17 seconds total)