Starting phenix.real_space_refine on Thu Feb 13 20:37:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qpc_4613/02_2025/6qpc_4613.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qpc_4613/02_2025/6qpc_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/cci-nas-00/data/ceres_data/6qpc_4613/02_2025/6qpc_4613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qpc_4613/02_2025/6qpc_4613.map" model { file = "/net/cci-nas-00/data/ceres_data/6qpc_4613/02_2025/6qpc_4613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qpc_4613/02_2025/6qpc_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 8.35, per 1000 atoms: 0.91 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: 2.44 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.76 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: 2.64 Time building geometry restraints manager: 2.71 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: 0.04 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: 0.670 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.370 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 29.410 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 1.116 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: 0.2091 time to fit residues: 63.1727 Evaluate side-chains 151 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.119287 restraints weight = 18559.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.121487 restraints weight = 11727.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.123040 restraints weight = 8779.874| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 to be fit. rotamer outliers: 17 poor density : 177 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: symmetry clash REVERT: A 517 SER cc_start: 0.9002 (p) cc_final: 0.8773 (t) REVERT: B 524 LEU cc_start: 0.8788 (tp) cc_final: 0.8512 (mt) outliers start: 17 outliers final: 11 residues processed: 187 average time/residue: 0.2144 time to fit residues: 58.2584 Evaluate side-chains 161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 74 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 17 optimal weight: 0.0010 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 B 695 ASN B 818 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.140561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119884 restraints weight = 18772.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.122190 restraints weight = 11911.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123554 restraints weight = 8813.049| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9372 Z= 0.190 Angle : 0.587 8.625 12734 Z= 0.315 Chirality : 0.040 0.144 1426 Planarity : 0.005 0.054 1564 Dihedral : 9.626 151.230 1306 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.54 % Allowed : 13.66 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.12 (0.23), residues: 1110 helix: 0.56 (0.17), residues: 760 sheet: None (None), residues: 0 loop : -1.38 (0.28), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 650 HIS 0.005 0.001 HIS A 818 PHE 0.023 0.002 PHE B 485 TYR 0.028 0.001 TYR B 477 ARG 0.003 0.000 ARG A 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 187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 1.005 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: 0.8271 (t80) cc_final: 0.7606 (t80) REVERT: A 322 LEU cc_start: 0.8389 (mm) cc_final: 0.7961 (tt) REVERT: B 305 TYR cc_start: 0.8294 (t80) cc_final: 0.7647 (t80) REVERT: B 474 ILE cc_start: 0.8264 (mm) cc_final: 0.7772 (mm) REVERT: B 598 PRO cc_start: 0.8088 (Cg_exo) cc_final: 0.7884 (Cg_endo) outliers start: 14 outliers final: 11 residues processed: 182 average time/residue: 0.1747 time to fit residues: 46.4135 Evaluate side-chains 165 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 59 optimal weight: 30.0000 chunk 60 optimal weight: 8.9990 chunk 42 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.138190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117285 restraints weight = 18705.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.119601 restraints weight = 12266.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.120905 restraints weight = 9030.271| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9372 Z= 0.276 Angle : 0.620 8.724 12734 Z= 0.331 Chirality : 0.041 0.149 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.539 150.162 1306 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.53 % Allowed : 15.42 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1110 helix: 0.75 (0.18), residues: 770 sheet: None (None), residues: 0 loop : -1.19 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 829 HIS 0.010 0.002 HIS B 818 PHE 0.029 0.002 PHE B 838 TYR 0.030 0.002 TYR B 477 ARG 0.003 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 174 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.996 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 821 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6482 (pp20) REVERT: A 826 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 322 LEU cc_start: 0.8412 (mm) cc_final: 0.7906 (tt) REVERT: B 598 PRO cc_start: 0.7904 (Cg_exo) cc_final: 0.7634 (Cg_endo) REVERT: B 821 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6467 (pm20) outliers start: 23 outliers final: 16 residues processed: 166 average time/residue: 0.1824 time to fit residues: 43.9066 Evaluate side-chains 161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 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 471 VAL Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 30.0000 chunk 70 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** 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 = 0.3974 r_free = 0.3974 target = 0.140466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.119167 restraints weight = 18772.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.121489 restraints weight = 11869.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.123032 restraints weight = 8822.570| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9372 Z= 0.189 Angle : 0.574 8.737 12734 Z= 0.305 Chirality : 0.040 0.143 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.418 152.034 1306 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.75 % Allowed : 16.74 % 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 : -1.01 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.010 0.001 HIS B 818 PHE 0.025 0.002 PHE B 838 TYR 0.026 0.001 TYR B 477 ARG 0.003 0.000 ARG B 753 *********************** 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 to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.999 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: 0.8298 (t80) cc_final: 0.7707 (t80) REVERT: A 322 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8010 (tt) REVERT: A 373 ILE cc_start: 0.8396 (mt) cc_final: 0.8185 (mt) REVERT: A 821 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6541 (pp20) REVERT: B 305 TYR cc_start: 0.8295 (t80) cc_final: 0.7644 (t80) REVERT: B 524 LEU cc_start: 0.8840 (tp) cc_final: 0.8471 (mt) REVERT: B 821 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6480 (pm20) outliers start: 25 outliers final: 14 residues processed: 176 average time/residue: 0.1728 time to fit residues: 44.4582 Evaluate side-chains 163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 322 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 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 543 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU 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 89 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 57 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.140703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.119424 restraints weight = 18662.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121762 restraints weight = 11863.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123067 restraints weight = 8816.330| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9372 Z= 0.199 Angle : 0.593 11.140 12734 Z= 0.308 Chirality : 0.040 0.140 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.311 151.928 1306 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.75 % Allowed : 17.62 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1110 helix: 1.11 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.89 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 829 HIS 0.009 0.001 HIS A 818 PHE 0.022 0.002 PHE B 838 TYR 0.027 0.001 TYR B 477 ARG 0.003 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 184 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.088 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: symmetry clash REVERT: A 322 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8049 (tt) REVERT: A 373 ILE cc_start: 0.8398 (mt) cc_final: 0.8179 (mt) REVERT: A 821 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6500 (pp20) REVERT: B 322 LEU cc_start: 0.8526 (mm) cc_final: 0.7974 (tt) REVERT: B 821 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6514 (pm20) outliers start: 25 outliers final: 13 residues processed: 176 average time/residue: 0.1854 time to fit residues: 47.7788 Evaluate side-chains 166 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 322 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 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 534 MET Chi-restraints excluded: chain B residue 543 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 9.9990 chunk 7 optimal weight: 0.0770 chunk 94 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.142374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.121288 restraints weight = 18907.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123647 restraints weight = 11825.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124986 restraints weight = 8740.815| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9372 Z= 0.169 Angle : 0.576 10.543 12734 Z= 0.298 Chirality : 0.040 0.143 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.186 152.770 1306 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.42 % Allowed : 18.50 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1110 helix: 1.22 (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 0.022 0.001 TRP B 650 HIS 0.008 0.001 HIS B 818 PHE 0.020 0.001 PHE B 838 TYR 0.027 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 187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.046 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 305 TYR cc_start: 0.8259 (t80) cc_final: 0.7901 (t80) REVERT: A 322 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 373 ILE cc_start: 0.8337 (mt) cc_final: 0.8023 (mt) REVERT: A 477 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6346 (p90) REVERT: A 821 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6438 (pm20) REVERT: A 842 MET cc_start: 0.8452 (ttt) cc_final: 0.8245 (ttt) REVERT: B 305 TYR cc_start: 0.8297 (t80) cc_final: 0.7672 (t80) REVERT: B 322 LEU cc_start: 0.8442 (mm) cc_final: 0.7934 (tt) REVERT: B 373 ILE cc_start: 0.8429 (mt) cc_final: 0.8140 (mt) REVERT: B 524 LEU cc_start: 0.8773 (tp) cc_final: 0.8477 (mt) REVERT: B 821 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6479 (pm20) outliers start: 22 outliers final: 9 residues processed: 180 average time/residue: 0.1859 time to fit residues: 48.8471 Evaluate side-chains 169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 322 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 609 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.120790 restraints weight = 19055.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.122849 restraints weight = 12015.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.124479 restraints weight = 9086.875| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9372 Z= 0.211 Angle : 0.610 10.516 12734 Z= 0.319 Chirality : 0.041 0.172 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.138 152.068 1306 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.09 % Allowed : 19.71 % Favored : 78.19 % 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: 0.90 (0.24), residues: 1110 helix: 1.23 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.79 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 650 HIS 0.009 0.001 HIS B 818 PHE 0.019 0.001 PHE B 838 TYR 0.027 0.001 TYR B 477 ARG 0.003 0.000 ARG A 753 *********************** 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 177 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.051 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 322 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 373 ILE cc_start: 0.8332 (mt) cc_final: 0.8005 (mt) REVERT: A 477 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.6266 (p90) REVERT: A 553 MET cc_start: 0.8128 (tpp) cc_final: 0.7833 (tpp) REVERT: A 821 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: B 305 TYR cc_start: 0.8229 (t80) cc_final: 0.7832 (t80) REVERT: B 322 LEU cc_start: 0.8375 (mm) cc_final: 0.7895 (tt) REVERT: B 373 ILE cc_start: 0.8419 (mt) cc_final: 0.8121 (mt) REVERT: B 821 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6492 (pm20) outliers start: 19 outliers final: 11 residues processed: 172 average time/residue: 0.1874 time to fit residues: 46.3879 Evaluate side-chains 162 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 322 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 557 LEU Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 57 optimal weight: 30.0000 chunk 96 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 50 optimal weight: 0.0000 chunk 95 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.143726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122945 restraints weight = 18711.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124998 restraints weight = 11989.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.126692 restraints weight = 9109.221| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9372 Z= 0.172 Angle : 0.594 11.637 12734 Z= 0.308 Chirality : 0.040 0.198 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.084 152.861 1306 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.98 % Allowed : 20.81 % Favored : 77.20 % 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: 0.99 (0.24), residues: 1110 helix: 1.30 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.76 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 650 HIS 0.010 0.001 HIS B 818 PHE 0.020 0.001 PHE B 838 TYR 0.027 0.001 TYR B 477 ARG 0.002 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 182 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.066 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 305 TYR cc_start: 0.8225 (t80) cc_final: 0.7991 (t80) REVERT: A 322 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7997 (tt) REVERT: A 373 ILE cc_start: 0.8320 (mt) cc_final: 0.7971 (mt) REVERT: A 477 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.6253 (p90) REVERT: A 553 MET cc_start: 0.8082 (tpp) cc_final: 0.7749 (tpp) REVERT: A 821 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6395 (pm20) REVERT: B 305 TYR cc_start: 0.8240 (t80) cc_final: 0.7602 (t80) REVERT: B 322 LEU cc_start: 0.8362 (mm) cc_final: 0.7884 (tt) REVERT: B 373 ILE cc_start: 0.8500 (mt) cc_final: 0.8160 (mt) REVERT: B 553 MET cc_start: 0.8113 (tpp) cc_final: 0.7796 (tpp) REVERT: B 821 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6473 (pm20) outliers start: 18 outliers final: 11 residues processed: 178 average time/residue: 0.1820 time to fit residues: 47.4460 Evaluate side-chains 171 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 322 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 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 696 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 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN ** B 696 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 = 0.3998 r_free = 0.3998 target = 0.142477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.121579 restraints weight = 18907.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.123605 restraints weight = 12073.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.125284 restraints weight = 9184.663| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3331 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= 0.210 Angle : 0.610 12.244 12734 Z= 0.316 Chirality : 0.041 0.189 1426 Planarity : 0.005 0.053 1564 Dihedral : 9.056 151.841 1306 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.09 % Allowed : 21.04 % 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: 1.05 (0.24), residues: 1110 helix: 1.35 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.73 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 650 HIS 0.010 0.001 HIS B 818 PHE 0.019 0.001 PHE B 838 TYR 0.025 0.001 TYR B 477 ARG 0.002 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 175 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.038 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 322 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 373 ILE cc_start: 0.8363 (mt) cc_final: 0.8012 (mt) REVERT: A 477 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.6196 (p90) REVERT: A 553 MET cc_start: 0.8150 (tpp) cc_final: 0.7883 (tpp) REVERT: A 821 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6471 (pm20) REVERT: B 322 LEU cc_start: 0.8328 (mm) cc_final: 0.7872 (tt) REVERT: B 373 ILE cc_start: 0.8476 (mt) cc_final: 0.8153 (mt) REVERT: B 386 MET cc_start: 0.7633 (tpt) cc_final: 0.7318 (tpt) REVERT: B 553 MET cc_start: 0.8134 (tpp) cc_final: 0.7855 (tpp) REVERT: B 821 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6458 (pm20) outliers start: 19 outliers final: 15 residues processed: 170 average time/residue: 0.1834 time to fit residues: 45.2995 Evaluate side-chains 168 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 322 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 557 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 821 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 696 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 91 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 4 optimal weight: 0.0000 chunk 33 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.143933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.123166 restraints weight = 18693.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.125403 restraints weight = 11958.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.126751 restraints weight = 8948.407| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9372 Z= 0.175 Angle : 0.603 12.000 12734 Z= 0.313 Chirality : 0.041 0.177 1426 Planarity : 0.005 0.052 1564 Dihedral : 9.039 152.581 1306 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.87 % Allowed : 21.26 % 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: 1.10 (0.24), residues: 1110 helix: 1.37 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.68 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 650 HIS 0.010 0.001 HIS B 818 PHE 0.019 0.001 PHE B 838 TYR 0.026 0.001 TYR B 477 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: 2658.18 seconds wall clock time: 48 minutes 38.99 seconds (2918.99 seconds total)