Starting phenix.real_space_refine on Wed Sep 25 03:01:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/09_2024/6qpc_4613.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/09_2024/6qpc_4613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/09_2024/6qpc_4613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/09_2024/6qpc_4613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/09_2024/6qpc_4613.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qpc_4613/09_2024/6qpc_4613.cif" } resolution = 3.5 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= 0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 62 5.16 5 C 6040 2.51 5 N 1454 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9140 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4530 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 28, 'TRANS': 548} Chain breaks: 10 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 126 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'P1O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 7.97, per 1000 atoms: 0.87 Number of scatterers: 9140 At special positions: 0 Unit cell: (94.116, 110.308, 109.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 62 16.00 P 2 15.00 O 1578 8.00 N 1454 7.00 C 6040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.02 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 952.5 milliseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 2 sheets defined 70.3% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.556A pdb=" N ARG A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.533A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.914A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 375 removed outlier: 4.376A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 404 removed outlier: 3.620A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 487 removed outlier: 3.667A pdb=" N ILE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 539 Processing helix chain 'A' and resid 543 through 573 removed outlier: 4.855A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 637 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.656A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 687 through 710 removed outlier: 3.854A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.750A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.516A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.600A pdb=" N ASN A 779 " --> pdb=" O GLY A 775 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 265 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.533A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.914A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 375 removed outlier: 4.375A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 404 removed outlier: 3.620A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 487 removed outlier: 3.666A pdb=" N ILE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 Processing helix chain 'B' and resid 543 through 573 removed outlier: 4.854A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 637 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.657A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 687 through 710 removed outlier: 3.855A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.751A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 removed outlier: 3.516A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.601A pdb=" N ASN B 779 " --> pdb=" O GLY B 775 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing sheet with id=AA1, first strand: chain 'A' and resid 782 through 783 Processing sheet with id=AA2, first strand: chain 'B' and resid 782 through 783 592 hydrogen bonds defined for protein. 1758 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: 2.42 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1464 1.32 - 1.45: 2722 1.45 - 1.58: 5080 1.58 - 1.71: 6 1.71 - 1.83: 100 Bond restraints: 9372 Sorted by residual: bond pdb=" O3 P1O A1003 " pdb=" P1 P1O A1003 " ideal model delta sigma weight residual 1.648 1.770 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" O3 P1O B1003 " pdb=" P1 P1O B1003 " ideal model delta sigma weight residual 1.648 1.770 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C19 P1O A1003 " pdb=" C20 P1O A1003 " ideal model delta sigma weight residual 1.502 1.584 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C19 P1O B1003 " pdb=" C20 P1O B1003 " ideal model delta sigma weight residual 1.502 1.583 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 P1O B1003 " pdb=" C2 P1O B1003 " ideal model delta sigma weight residual 1.513 1.589 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 9367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 12234 2.26 - 4.52: 418 4.52 - 6.78: 50 6.78 - 9.04: 26 9.04 - 11.30: 6 Bond angle restraints: 12734 Sorted by residual: angle pdb=" CA TYR A 477 " pdb=" CB TYR A 477 " pdb=" CG TYR A 477 " ideal model delta sigma weight residual 113.90 122.44 -8.54 1.80e+00 3.09e-01 2.25e+01 angle pdb=" CA TYR B 477 " pdb=" CB TYR B 477 " pdb=" CG TYR B 477 " ideal model delta sigma weight residual 113.90 122.42 -8.52 1.80e+00 3.09e-01 2.24e+01 angle pdb=" C LEU B 503 " pdb=" N THR B 504 " pdb=" CA THR B 504 " ideal model delta sigma weight residual 121.62 128.96 -7.34 1.57e+00 4.06e-01 2.18e+01 angle pdb=" C LEU A 503 " pdb=" N THR A 504 " pdb=" CA THR A 504 " ideal model delta sigma weight residual 121.62 128.94 -7.32 1.57e+00 4.06e-01 2.17e+01 angle pdb=" C VAL A 484 " pdb=" N PHE A 485 " pdb=" CA PHE A 485 " ideal model delta sigma weight residual 120.29 113.76 6.53 1.42e+00 4.96e-01 2.11e+01 ... (remaining 12729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.87: 5242 27.87 - 55.73: 222 55.73 - 83.60: 17 83.60 - 111.47: 2 111.47 - 139.34: 2 Dihedral angle restraints: 5485 sinusoidal: 2085 harmonic: 3400 Sorted by residual: dihedral pdb=" CA ARG A 354 " pdb=" C ARG A 354 " pdb=" N LEU A 355 " pdb=" CA LEU A 355 " ideal model delta harmonic sigma weight residual -180.00 -131.65 -48.35 0 5.00e+00 4.00e-02 9.35e+01 dihedral pdb=" CA ARG B 354 " pdb=" C ARG B 354 " pdb=" N LEU B 355 " pdb=" CA LEU B 355 " ideal model delta harmonic sigma weight residual 180.00 -131.70 -48.30 0 5.00e+00 4.00e-02 9.33e+01 dihedral pdb=" CA CYS A 356 " pdb=" C CYS A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual -180.00 -142.63 -37.37 0 5.00e+00 4.00e-02 5.59e+01 ... (remaining 5482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.016: 1424 1.016 - 2.032: 0 2.032 - 3.048: 0 3.048 - 4.064: 0 4.064 - 5.080: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C7 P1O B1003 " pdb=" C6 P1O B1003 " pdb=" C8 P1O B1003 " pdb=" O7 P1O B1003 " both_signs ideal model delta sigma weight residual False -2.35 2.73 -5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C7 P1O A1003 " pdb=" C6 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " both_signs ideal model delta sigma weight residual False -2.35 2.73 -5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" CB VAL A 531 " pdb=" CA VAL A 531 " pdb=" CG1 VAL A 531 " pdb=" CG2 VAL A 531 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1423 not shown) Planarity restraints: 1564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 670 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C GLU A 670 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU A 670 " -0.019 2.00e-02 2.50e+03 pdb=" N MET A 671 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 670 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.36e+00 pdb=" C GLU B 670 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU B 670 " 0.019 2.00e-02 2.50e+03 pdb=" N MET B 671 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 668 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C TYR A 668 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR A 668 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 669 " 0.017 2.00e-02 2.50e+03 ... (remaining 1561 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 117 2.60 - 3.17: 7670 3.17 - 3.75: 15191 3.75 - 4.32: 19670 4.32 - 4.90: 32383 Nonbonded interactions: 75031 Sorted by model distance: nonbonded pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 331 " pdb=" SG CYS B 372 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 352 " pdb=" SG CYS B 356 " model vdw 2.037 3.760 ... (remaining 75026 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' 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: 0.890 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.640 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.009 0.122 9372 Z= 0.544 Angle : 1.011 11.295 12734 Z= 0.549 Chirality : 0.198 5.080 1426 Planarity : 0.009 0.069 1564 Dihedral : 15.204 139.337 3270 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.22 % Allowed : 6.06 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.19 % 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: -3.36 (0.19), residues: 1110 helix: -2.06 (0.14), residues: 760 sheet: None (None), residues: 0 loop : -2.19 (0.26), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 397 HIS 0.004 0.001 HIS A 830 PHE 0.032 0.003 PHE B 685 TYR 0.042 0.003 TYR B 580 ARG 0.004 0.001 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.8079 (tt0) cc_final: 0.7755 (tt0) REVERT: A 355 LEU cc_start: 0.5820 (tp) cc_final: 0.5102 (pt) REVERT: A 524 LEU cc_start: 0.8983 (tp) cc_final: 0.8671 (mt) REVERT: A 534 MET cc_start: 0.7100 (mtm) cc_final: 0.6763 (mtt) REVERT: A 650 TRP cc_start: 0.7373 (p90) cc_final: 0.6969 (p90) REVERT: A 695 ASN cc_start: 0.8817 (t0) cc_final: 0.8504 (t0) REVERT: A 730 GLN cc_start: 0.8584 (mt0) cc_final: 0.8269 (mm-40) REVERT: A 818 HIS cc_start: 0.6650 (t-90) cc_final: 0.6259 (t70) REVERT: B 294 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6223 (mm-30) REVERT: B 355 LEU cc_start: 0.5826 (tp) cc_final: 0.5268 (pt) REVERT: B 534 MET cc_start: 0.6973 (mtm) cc_final: 0.6652 (ptt) REVERT: B 650 TRP cc_start: 0.7392 (p90) cc_final: 0.6960 (p90) REVERT: B 661 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8274 (mmmm) REVERT: B 730 GLN cc_start: 0.8561 (mt0) cc_final: 0.8262 (mm-40) outliers start: 2 outliers final: 2 residues processed: 216 average time/residue: 0.1982 time to fit residues: 59.4483 Evaluate side-chains 151 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 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 544 GLN A 608 GLN A 695 ASN A 730 GLN B 544 GLN B 608 GLN B 695 ASN B 730 GLN B 818 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9372 Z= 0.204 Angle : 0.639 8.578 12734 Z= 0.341 Chirality : 0.040 0.149 1426 Planarity : 0.006 0.057 1564 Dihedral : 10.100 149.827 1308 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.87 % Allowed : 11.01 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.19 % 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: -1.07 (0.22), residues: 1110 helix: -0.17 (0.16), residues: 750 sheet: None (None), residues: 0 loop : -1.69 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 829 HIS 0.008 0.001 HIS B 818 PHE 0.027 0.002 PHE B 485 TYR 0.031 0.002 TYR B 477 ARG 0.004 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 LEU cc_start: 0.8927 (tp) cc_final: 0.8699 (mt) REVERT: A 650 TRP cc_start: 0.7249 (p90) cc_final: 0.6991 (p90) REVERT: A 695 ASN cc_start: 0.8675 (t0) cc_final: 0.8458 (t0) REVERT: A 730 GLN cc_start: 0.8504 (mt0) cc_final: 0.8294 (mm-40) REVERT: B 265 GLU cc_start: 0.8051 (tt0) cc_final: 0.7628 (tt0) REVERT: B 267 TYR cc_start: 0.7077 (t80) cc_final: 0.6812 (t80) REVERT: B 311 LEU cc_start: 0.8621 (tp) cc_final: 0.8419 (tp) REVERT: B 524 LEU cc_start: 0.8881 (tp) cc_final: 0.8535 (mt) REVERT: B 650 TRP cc_start: 0.7271 (p90) cc_final: 0.6952 (p90) outliers start: 17 outliers final: 11 residues processed: 187 average time/residue: 0.1859 time to fit residues: 49.9140 Evaluate side-chains 163 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 694 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 30.0000 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 HIS B 608 GLN B 695 ASN B 818 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9372 Z= 0.379 Angle : 0.687 8.753 12734 Z= 0.367 Chirality : 0.043 0.154 1426 Planarity : 0.006 0.052 1564 Dihedral : 9.768 148.760 1306 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.20 % Allowed : 14.76 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1110 helix: 0.40 (0.17), residues: 760 sheet: None (None), residues: 0 loop : -1.45 (0.28), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 273 HIS 0.006 0.001 HIS A 818 PHE 0.026 0.002 PHE B 485 TYR 0.031 0.002 TYR A 477 ARG 0.004 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 LEU cc_start: 0.9021 (tp) cc_final: 0.8757 (mt) REVERT: A 650 TRP cc_start: 0.7337 (p90) cc_final: 0.7064 (p90) REVERT: A 695 ASN cc_start: 0.8734 (t0) cc_final: 0.8466 (t0) REVERT: A 730 GLN cc_start: 0.8605 (mt0) cc_final: 0.8371 (mm-40) REVERT: B 267 TYR cc_start: 0.7261 (t80) cc_final: 0.7002 (t80) REVERT: B 474 ILE cc_start: 0.8601 (mm) cc_final: 0.8189 (mm) REVERT: B 565 SER cc_start: 0.9039 (t) cc_final: 0.8752 (p) REVERT: B 842 MET cc_start: 0.8826 (ttt) cc_final: 0.8465 (ttt) outliers start: 20 outliers final: 14 residues processed: 165 average time/residue: 0.1785 time to fit residues: 42.9627 Evaluate side-chains 159 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 695 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9372 Z= 0.177 Angle : 0.580 8.721 12734 Z= 0.309 Chirality : 0.040 0.144 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.612 151.913 1306 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.98 % Allowed : 15.53 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1110 helix: 0.77 (0.18), residues: 766 sheet: None (None), residues: 0 loop : -1.13 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 397 HIS 0.013 0.002 HIS A 818 PHE 0.021 0.002 PHE B 485 TYR 0.028 0.001 TYR A 477 ARG 0.002 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.8352 (t80) cc_final: 0.7591 (t80) REVERT: A 348 MET cc_start: 0.7607 (ptm) cc_final: 0.7087 (ppp) REVERT: A 355 LEU cc_start: 0.5903 (tp) cc_final: 0.5695 (tp) REVERT: A 821 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: A 842 MET cc_start: 0.8743 (ttt) cc_final: 0.8496 (ttt) REVERT: B 267 TYR cc_start: 0.7180 (t80) cc_final: 0.6932 (t80) REVERT: B 305 TYR cc_start: 0.8339 (t80) cc_final: 0.7574 (t80) REVERT: B 322 LEU cc_start: 0.8554 (mm) cc_final: 0.7908 (tt) REVERT: B 355 LEU cc_start: 0.6059 (tp) cc_final: 0.5783 (tp) REVERT: B 474 ILE cc_start: 0.8466 (mm) cc_final: 0.7941 (mm) REVERT: B 565 SER cc_start: 0.8915 (t) cc_final: 0.8615 (p) REVERT: B 821 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: B 842 MET cc_start: 0.8788 (ttt) cc_final: 0.8403 (ttt) outliers start: 18 outliers final: 11 residues processed: 187 average time/residue: 0.1773 time to fit residues: 48.5752 Evaluate side-chains 166 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 1 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9372 Z= 0.204 Angle : 0.593 8.743 12734 Z= 0.316 Chirality : 0.040 0.146 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.446 151.248 1306 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.42 % Allowed : 17.07 % Favored : 80.51 % 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 (0.24), residues: 1110 helix: 0.96 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.00 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.004 0.001 HIS A 818 PHE 0.020 0.002 PHE B 485 TYR 0.025 0.001 TYR B 477 ARG 0.003 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8217 (mp) REVERT: B 267 TYR cc_start: 0.7249 (t80) cc_final: 0.7015 (t80) REVERT: B 355 LEU cc_start: 0.5987 (tp) cc_final: 0.5750 (tp) REVERT: B 821 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6700 (pm20) REVERT: B 842 MET cc_start: 0.8811 (ttt) cc_final: 0.8519 (ttt) outliers start: 22 outliers final: 13 residues processed: 178 average time/residue: 0.1714 time to fit residues: 45.0610 Evaluate side-chains 167 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.0870 chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 30.0000 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN B 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9372 Z= 0.188 Angle : 0.579 8.710 12734 Z= 0.308 Chirality : 0.040 0.146 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.331 152.039 1306 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.75 % Allowed : 19.16 % Favored : 78.08 % 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: 0.76 (0.24), residues: 1110 helix: 1.20 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.97 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 650 HIS 0.002 0.001 HIS B 818 PHE 0.019 0.001 PHE B 485 TYR 0.027 0.001 TYR B 477 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.8385 (t80) cc_final: 0.7907 (t80) REVERT: A 821 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6655 (pp20) REVERT: A 826 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 842 MET cc_start: 0.8729 (ttt) cc_final: 0.8144 (ttt) REVERT: B 267 TYR cc_start: 0.7279 (t80) cc_final: 0.7038 (t80) REVERT: B 305 TYR cc_start: 0.8386 (t80) cc_final: 0.7732 (t80) REVERT: B 322 LEU cc_start: 0.8676 (mm) cc_final: 0.7997 (tt) REVERT: B 821 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6662 (pm20) REVERT: B 842 MET cc_start: 0.8760 (ttt) cc_final: 0.8426 (ttt) outliers start: 25 outliers final: 13 residues processed: 177 average time/residue: 0.1688 time to fit residues: 43.7173 Evaluate side-chains 168 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 0.0170 chunk 67 optimal weight: 2.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9372 Z= 0.179 Angle : 0.588 11.355 12734 Z= 0.309 Chirality : 0.040 0.157 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.249 152.298 1306 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.08 % Allowed : 19.16 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1110 helix: 1.26 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.88 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 650 HIS 0.002 0.001 HIS A 844 PHE 0.017 0.001 PHE B 485 TYR 0.025 0.001 TYR B 477 ARG 0.002 0.000 ARG B 753 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 ILE cc_start: 0.8453 (mt) cc_final: 0.8191 (mt) REVERT: A 553 MET cc_start: 0.8110 (tpp) cc_final: 0.7621 (tpp) REVERT: A 821 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: A 842 MET cc_start: 0.8702 (ttt) cc_final: 0.8316 (ttt) REVERT: B 267 TYR cc_start: 0.7256 (t80) cc_final: 0.7007 (t80) REVERT: B 322 LEU cc_start: 0.8664 (mm) cc_final: 0.8013 (tt) REVERT: B 821 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: B 826 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8177 (mp) REVERT: B 842 MET cc_start: 0.8794 (ttt) cc_final: 0.8453 (ttt) outliers start: 28 outliers final: 16 residues processed: 184 average time/residue: 0.1809 time to fit residues: 49.0355 Evaluate side-chains 174 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9372 Z= 0.183 Angle : 0.604 11.227 12734 Z= 0.314 Chirality : 0.041 0.169 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.177 152.263 1306 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.64 % Allowed : 19.49 % Favored : 77.86 % 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: 0.91 (0.24), residues: 1110 helix: 1.30 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.88 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 650 HIS 0.002 0.001 HIS A 818 PHE 0.017 0.001 PHE B 485 TYR 0.024 0.001 TYR B 477 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 ILE cc_start: 0.8380 (mt) cc_final: 0.8087 (mt) REVERT: A 477 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6581 (p90) REVERT: A 553 MET cc_start: 0.8107 (tpp) cc_final: 0.7617 (tpp) REVERT: A 661 LYS cc_start: 0.8256 (pttt) cc_final: 0.8038 (mmmm) REVERT: A 821 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6619 (pm20) REVERT: A 826 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 842 MET cc_start: 0.8696 (ttt) cc_final: 0.8464 (ttt) REVERT: B 267 TYR cc_start: 0.7261 (t80) cc_final: 0.7007 (t80) REVERT: B 322 LEU cc_start: 0.8635 (mm) cc_final: 0.8033 (tt) REVERT: B 386 MET cc_start: 0.7782 (tpt) cc_final: 0.7346 (tpt) REVERT: B 821 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6653 (pm20) REVERT: B 842 MET cc_start: 0.8673 (ttt) cc_final: 0.8401 (ttt) outliers start: 24 outliers final: 17 residues processed: 185 average time/residue: 0.1813 time to fit residues: 48.4819 Evaluate side-chains 175 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9372 Z= 0.213 Angle : 0.628 11.294 12734 Z= 0.325 Chirality : 0.042 0.181 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.143 151.660 1306 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.97 % Allowed : 20.15 % Favored : 76.87 % 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: 0.95 (0.24), residues: 1110 helix: 1.33 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 650 HIS 0.002 0.001 HIS A 818 PHE 0.017 0.001 PHE B 485 TYR 0.025 0.001 TYR B 477 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 ILE cc_start: 0.8451 (mt) cc_final: 0.8162 (mt) REVERT: A 477 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6654 (p90) REVERT: A 553 MET cc_start: 0.8080 (tpp) cc_final: 0.7637 (tpp) REVERT: A 661 LYS cc_start: 0.8270 (pttt) cc_final: 0.8047 (mmmm) REVERT: A 821 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: A 826 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 842 MET cc_start: 0.8695 (ttt) cc_final: 0.8493 (ttt) REVERT: B 267 TYR cc_start: 0.7322 (t80) cc_final: 0.7059 (t80) REVERT: B 386 MET cc_start: 0.7812 (tpt) cc_final: 0.7430 (tpt) REVERT: B 821 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6635 (pm20) REVERT: B 842 MET cc_start: 0.8724 (ttt) cc_final: 0.8490 (ttt) outliers start: 27 outliers final: 20 residues processed: 175 average time/residue: 0.1725 time to fit residues: 44.4905 Evaluate side-chains 175 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN B 695 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9372 Z= 0.276 Angle : 0.670 12.135 12734 Z= 0.344 Chirality : 0.043 0.192 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.175 150.681 1306 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.75 % Allowed : 20.48 % Favored : 76.76 % 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: 0.89 (0.24), residues: 1110 helix: 1.23 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.82 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 650 HIS 0.003 0.001 HIS A 830 PHE 0.017 0.002 PHE B 760 TYR 0.026 0.002 TYR B 528 ARG 0.003 0.000 ARG B 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.7897 (tpt) cc_final: 0.7693 (tpt) REVERT: A 477 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6714 (p90) REVERT: A 553 MET cc_start: 0.8212 (tpp) cc_final: 0.7743 (tpp) REVERT: A 661 LYS cc_start: 0.8361 (pttt) cc_final: 0.8099 (mmmm) REVERT: A 821 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6732 (pm20) REVERT: A 826 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 267 TYR cc_start: 0.7387 (t80) cc_final: 0.7109 (t80) REVERT: B 386 MET cc_start: 0.7863 (tpt) cc_final: 0.7559 (tpt) REVERT: B 821 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6740 (pm20) REVERT: B 842 MET cc_start: 0.8676 (ttt) cc_final: 0.8416 (ttt) outliers start: 25 outliers final: 16 residues processed: 168 average time/residue: 0.1834 time to fit residues: 45.1325 Evaluate side-chains 167 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN ** B 818 HIS ** 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 = 0.3993 r_free = 0.3993 target = 0.142126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.121431 restraints weight = 18623.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.123671 restraints weight = 11927.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.125156 restraints weight = 8902.091| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9372 Z= 0.196 Angle : 0.648 12.634 12734 Z= 0.329 Chirality : 0.042 0.183 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.169 151.950 1306 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.75 % Allowed : 20.70 % Favored : 76.54 % 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: 0.98 (0.24), residues: 1110 helix: 1.35 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.84 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 650 HIS 0.002 0.001 HIS B 818 PHE 0.016 0.001 PHE B 485 TYR 0.025 0.001 TYR B 528 ARG 0.002 0.000 ARG B 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1852.54 seconds wall clock time: 33 minutes 49.09 seconds (2029.09 seconds total)