Starting phenix.real_space_refine on Fri Sep 11 12:28:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qpc_4613/09_2026/6qpc_4613.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qpc_4613/09_2026/6qpc_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6qpc_4613/09_2026/6qpc_4613.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qpc_4613/09_2026/6qpc_4613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qpc_4613/09_2026/6qpc_4613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qpc_4613/09_2026/6qpc_4613.map" model { file = "/net/cci-nas-00/data/ceres_data/6qpc_4613/09_2026/6qpc_4613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qpc_4613/09_2026/6qpc_4613.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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, 'ARG:plan': 6, 'TYR:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 4, 'HIS:plan': 2, 'TRP:plan': 1} 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: 3.59, per 1000 atoms: 0.39 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=10, 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 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.02 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 369.3 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: 0.20 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: 1.31 Time building geometry restraints manager: 1.15 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 - 16.74: 4850 16.74 - 33.48: 475 33.48 - 50.22: 127 50.22 - 66.96: 20 66.96 - 83.70: 10 Dihedral angle restraints: 5482 sinusoidal: 2082 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 5479 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: 2.18 - 2.72: 516 2.72 - 3.27: 9447 3.27 - 3.81: 15769 3.81 - 4.36: 18137 4.36 - 4.90: 31147 Nonbonded interactions: 75016 Sorted by model distance: nonbonded pdb=" O VAL A 561 " pdb=" OG SER A 565 " model vdw 2.176 3.040 nonbonded pdb=" O VAL B 561 " pdb=" OG SER B 565 " model vdw 2.178 3.040 nonbonded pdb=" O ALA B 508 " pdb=" OG1 THR B 512 " model vdw 2.290 3.040 nonbonded pdb=" O ALA A 508 " pdb=" OG1 THR A 512 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR A 364 " pdb=" OG SER A 367 " model vdw 2.304 3.040 ... (remaining 75011 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: 0.02 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.880 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 9384 Z= 0.393 Angle : 1.016 11.295 12754 Z= 0.551 Chirality : 0.198 5.080 1426 Planarity : 0.009 0.069 1564 Dihedral : 14.711 83.699 3252 Min Nonbonded Distance : 2.176 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG B 252 TYR 0.042 0.003 TYR B 580 PHE 0.032 0.003 PHE B 685 TRP 0.017 0.003 TRP A 397 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.39 ( 9372) covalent geometry : angle 1.01130 / 0.55 (12734) SS BOND : bond 0.00618 / 0.39 ( 10) SS BOND : angle 2.70478 / 1.84 ( 20) hydrogen bonds : bond 0.12833 / 9.01 ( 592) hydrogen bonds : angle 7.51760 / 5.38 ( 1758) Misc. bond : bond 0.00175 / 0.09 ( 2) *********************** 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 : 0.352 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: 0.8816 (t0) cc_final: 0.8504 (t0) REVERT: A 730 GLN cc_start: 0.8584 (mt0) cc_final: 0.8268 (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: 0.6653 (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: 0.0880 time to fit residues: 26.8748 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 : 0.381 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3987 r_free = 0.3987 target = 0.141213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119768 restraints weight = 18682.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.122217 restraints weight = 11881.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123595 restraints weight = 8767.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124653 restraints weight = 7307.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.125161 restraints weight = 6424.228| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9384 Z= 0.150 Angle : 0.639 8.584 12754 Z= 0.339 Chirality : 0.040 0.152 1426 Planarity : 0.006 0.058 1564 Dihedral : 7.491 54.575 1290 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.76 % Allowed : 10.90 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.21), residues: 1110 helix: -0.23 (0.16), residues: 750 sheet: None (None), residues: 0 loop : -1.68 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 753 TYR 0.030 0.002 TYR B 477 PHE 0.027 0.002 PHE B 485 TRP 0.011 0.001 TRP A 829 HIS 0.007 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 9372) covalent geometry : angle 0.63714 / 0.34 (12734) SS BOND : bond 0.00212 / 0.13 ( 10) SS BOND : angle 1.35383 / 1.00 ( 20) hydrogen bonds : bond 0.05232 / 3.72 ( 592) hydrogen bonds : angle 5.33439 / 3.84 ( 1758) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** 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 192 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.313 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 517 SER cc_start: 0.8985 (p) cc_final: 0.8761 (t) REVERT: B 524 LEU cc_start: 0.8794 (tp) cc_final: 0.8529 (mt) outliers start: 16 outliers final: 12 residues processed: 186 average time/residue: 0.0793 time to fit residues: 21.6366 Evaluate side-chains 158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 365 CYS 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 13 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS B 608 GLN B 695 ASN B 818 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.138502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116719 restraints weight = 18868.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.118956 restraints weight = 11954.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.120252 restraints weight = 8971.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.121333 restraints weight = 7537.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121810 restraints weight = 6650.471| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9384 Z= 0.198 Angle : 0.632 8.683 12754 Z= 0.338 Chirality : 0.041 0.149 1426 Planarity : 0.005 0.054 1564 Dihedral : 6.925 53.618 1288 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.71 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 : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1110 helix: 0.46 (0.17), residues: 766 sheet: None (None), residues: 0 loop : -1.38 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 753 TYR 0.029 0.002 TYR B 477 PHE 0.024 0.002 PHE B 485 TRP 0.024 0.002 TRP A 650 HIS 0.005 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 9372) covalent geometry : angle 0.63150 / 0.34 (12734) SS BOND : bond 0.00319 / 0.19 ( 10) SS BOND : angle 1.06994 / 0.77 ( 20) hydrogen bonds : bond 0.05159 / 3.68 ( 592) hydrogen bonds : angle 5.02169 / 3.61 ( 1758) Misc. bond : bond 0.00047 / 0.02 ( 2) *********************** 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 177 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.367 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 355 LEU cc_start: 0.5875 (tp) cc_final: 0.5341 (pt) REVERT: A 517 SER cc_start: 0.9036 (p) cc_final: 0.8833 (t) REVERT: B 355 LEU cc_start: 0.6033 (tp) cc_final: 0.5540 (pt) REVERT: B 474 ILE cc_start: 0.8259 (mm) cc_final: 0.7841 (mm) REVERT: B 534 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6371 (ptp) outliers start: 20 outliers final: 14 residues processed: 168 average time/residue: 0.0752 time to fit residues: 19.0059 Evaluate side-chains 157 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 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 365 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 534 MET 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 80 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.0070 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 ASN B 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.140109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.119124 restraints weight = 19041.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.121355 restraints weight = 11996.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.122650 restraints weight = 8952.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123735 restraints weight = 7473.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.124117 restraints weight = 6564.050| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9384 Z= 0.153 Angle : 0.590 8.674 12754 Z= 0.315 Chirality : 0.040 0.147 1426 Planarity : 0.005 0.053 1564 Dihedral : 6.675 56.761 1288 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.23), residues: 1110 helix: 0.79 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.14 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 753 TYR 0.031 0.001 TYR B 477 PHE 0.021 0.002 PHE B 485 TRP 0.010 0.001 TRP A 650 HIS 0.006 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9372) covalent geometry : angle 0.58964 / 0.31 (12734) SS BOND : bond 0.00214 / 0.13 ( 10) SS BOND : angle 0.92292 / 0.67 ( 20) hydrogen bonds : bond 0.04812 / 3.42 ( 592) hydrogen bonds : angle 4.83458 / 3.46 ( 1758) Misc. bond : bond 0.00040 / 0.02 ( 2) *********************** 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 193 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.300 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: 0.8323 (t80) cc_final: 0.7663 (t80) REVERT: A 821 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6635 (pm20) REVERT: B 305 TYR cc_start: 0.8337 (t80) cc_final: 0.7661 (t80) REVERT: B 322 LEU cc_start: 0.8364 (mm) cc_final: 0.7898 (tt) REVERT: B 821 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6525 (pm20) outliers start: 23 outliers final: 17 residues processed: 186 average time/residue: 0.0657 time to fit residues: 18.4126 Evaluate side-chains 160 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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 365 CYS Chi-restraints excluded: chain B residue 372 CYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3989 r_free = 0.3989 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120251 restraints weight = 18808.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122110 restraints weight = 11991.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.123785 restraints weight = 9145.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124458 restraints weight = 7557.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.124969 restraints weight = 6812.078| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9384 Z= 0.138 Angle : 0.575 8.690 12754 Z= 0.307 Chirality : 0.040 0.141 1426 Planarity : 0.005 0.053 1564 Dihedral : 6.454 59.989 1288 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.75 % Allowed : 17.40 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1110 helix: 1.01 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -1.04 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 753 TYR 0.028 0.001 TYR B 477 PHE 0.020 0.002 PHE B 485 TRP 0.010 0.001 TRP A 397 HIS 0.003 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 9372) covalent geometry : angle 0.57450 / 0.31 (12734) SS BOND : bond 0.00195 / 0.12 ( 10) SS BOND : angle 1.01058 / 0.74 ( 20) hydrogen bonds : bond 0.04634 / 3.31 ( 592) hydrogen bonds : angle 4.68961 / 3.36 ( 1758) Misc. bond : bond 0.00030 / 0.02 ( 2) *********************** 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 193 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.422 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: 0.8350 (OUTLIER) cc_final: 0.8000 (tt) REVERT: A 373 ILE cc_start: 0.8361 (mt) cc_final: 0.8127 (mt) REVERT: A 517 SER cc_start: 0.9002 (p) cc_final: 0.8792 (t) REVERT: B 373 ILE cc_start: 0.8355 (mt) cc_final: 0.8089 (mt) REVERT: B 524 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8576 (mt) outliers start: 25 outliers final: 18 residues processed: 182 average time/residue: 0.0743 time to fit residues: 20.2119 Evaluate side-chains 169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 609 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 50 optimal weight: 0.0070 chunk 57 optimal weight: 30.0000 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 61 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 608 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.143668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123260 restraints weight = 18589.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.125365 restraints weight = 11694.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.126928 restraints weight = 8774.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127850 restraints weight = 7182.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.128287 restraints weight = 6336.174| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9384 Z= 0.122 Angle : 0.576 11.965 12754 Z= 0.297 Chirality : 0.039 0.143 1426 Planarity : 0.005 0.052 1564 Dihedral : 6.135 56.886 1288 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.64 % Allowed : 18.39 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1110 helix: 1.27 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -0.92 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 753 TYR 0.026 0.001 TYR B 477 PHE 0.029 0.001 PHE A 462 TRP 0.009 0.001 TRP A 650 HIS 0.004 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9372) covalent geometry : angle 0.57534 / 0.30 (12734) SS BOND : bond 0.00206 / 0.13 ( 10) SS BOND : angle 0.76159 / 0.56 ( 20) hydrogen bonds : bond 0.04370 / 3.13 ( 592) hydrogen bonds : angle 4.54162 / 3.24 ( 1758) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** 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 206 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.322 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: symmetry clash REVERT: A 305 TYR cc_start: 0.8305 (t80) cc_final: 0.7602 (t80) REVERT: A 322 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8011 (tt) REVERT: A 373 ILE cc_start: 0.8342 (mt) cc_final: 0.8042 (mt) REVERT: A 517 SER cc_start: 0.9039 (p) cc_final: 0.8831 (t) REVERT: B 305 TYR cc_start: 0.8271 (t80) cc_final: 0.7651 (t80) REVERT: B 322 LEU cc_start: 0.8411 (mm) cc_final: 0.7945 (tt) REVERT: B 373 ILE cc_start: 0.8312 (mt) cc_final: 0.7999 (mt) REVERT: B 524 LEU cc_start: 0.8819 (tp) cc_final: 0.8547 (mt) REVERT: B 821 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6310 (pm20) outliers start: 24 outliers final: 11 residues processed: 199 average time/residue: 0.0784 time to fit residues: 22.9470 Evaluate side-chains 178 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 B residue 269 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 10 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4001 r_free = 0.4001 target = 0.142674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.121628 restraints weight = 18833.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.123816 restraints weight = 12013.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125282 restraints weight = 9026.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.126121 restraints weight = 7505.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126769 restraints weight = 6692.655| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9384 Z= 0.150 Angle : 0.617 11.582 12754 Z= 0.322 Chirality : 0.041 0.145 1426 Planarity : 0.005 0.053 1564 Dihedral : 6.038 55.179 1288 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.75 % Allowed : 19.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1110 helix: 1.30 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -0.89 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 753 TYR 0.025 0.001 TYR B 477 PHE 0.026 0.002 PHE B 556 TRP 0.017 0.001 TRP B 650 HIS 0.003 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9372) covalent geometry : angle 0.61629 / 0.32 (12734) SS BOND : bond 0.00212 / 0.13 ( 10) SS BOND : angle 0.95566 / 0.70 ( 20) hydrogen bonds : bond 0.04505 / 3.23 ( 592) hydrogen bonds : angle 4.55707 / 3.25 ( 1758) Misc. bond : bond 0.00030 / 0.01 ( 2) *********************** 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 190 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.364 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: 0.8310 (OUTLIER) cc_final: 0.7980 (tt) REVERT: A 373 ILE cc_start: 0.8378 (mt) cc_final: 0.8047 (mt) REVERT: A 477 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.6238 (p90) REVERT: A 553 MET cc_start: 0.8049 (tpp) cc_final: 0.7756 (tpp) REVERT: B 305 TYR cc_start: 0.8332 (t80) cc_final: 0.7585 (t80) REVERT: B 322 LEU cc_start: 0.8417 (mm) cc_final: 0.7971 (tt) REVERT: B 373 ILE cc_start: 0.8355 (mt) cc_final: 0.8036 (mt) REVERT: B 524 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8516 (mt) REVERT: B 553 MET cc_start: 0.8074 (tpp) cc_final: 0.7738 (tpp) REVERT: B 753 ARG cc_start: 0.6733 (ptt90) cc_final: 0.6449 (ptt180) REVERT: B 821 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6291 (pm20) outliers start: 25 outliers final: 16 residues processed: 183 average time/residue: 0.0782 time to fit residues: 21.3108 Evaluate side-chains 174 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 543 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 524 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 609 LEU 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 64 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119682 restraints weight = 18795.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121563 restraints weight = 12064.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123223 restraints weight = 9301.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.124048 restraints weight = 7634.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.124444 restraints weight = 6802.348| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9384 Z= 0.184 Angle : 0.643 11.931 12754 Z= 0.335 Chirality : 0.042 0.147 1426 Planarity : 0.005 0.054 1564 Dihedral : 6.107 53.091 1288 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.64 % Allowed : 19.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1110 helix: 1.22 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.85 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 753 TYR 0.026 0.002 TYR B 477 PHE 0.023 0.002 PHE A 462 TRP 0.023 0.002 TRP A 650 HIS 0.005 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 9372) covalent geometry : angle 0.64255 / 0.33 (12734) SS BOND : bond 0.00262 / 0.16 ( 10) SS BOND : angle 0.96876 / 0.71 ( 20) hydrogen bonds : bond 0.04716 / 3.37 ( 592) hydrogen bonds : angle 4.67602 / 3.33 ( 1758) Misc. bond : bond 0.00032 / 0.02 ( 2) *********************** 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 176 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.349 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: 0.8318 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 373 ILE cc_start: 0.8364 (mt) cc_final: 0.8068 (mt) REVERT: A 477 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.6194 (p90) REVERT: A 553 MET cc_start: 0.8195 (tpp) cc_final: 0.7866 (tpp) REVERT: B 322 LEU cc_start: 0.8418 (mm) cc_final: 0.7959 (tt) REVERT: B 373 ILE cc_start: 0.8354 (mt) cc_final: 0.8021 (mt) REVERT: B 812 PHE cc_start: 0.7967 (m-80) cc_final: 0.7754 (m-80) REVERT: B 821 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6394 (pm20) outliers start: 24 outliers final: 18 residues processed: 170 average time/residue: 0.0806 time to fit residues: 20.4243 Evaluate side-chains 162 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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 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 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 609 LEU 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 34 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 814 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 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 = 0.3999 r_free = 0.3999 target = 0.142852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.121787 restraints weight = 18875.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.123837 restraints weight = 12019.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.125444 restraints weight = 9165.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126160 restraints weight = 7546.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126160 restraints weight = 6771.248| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9384 Z= 0.142 Angle : 0.614 11.197 12754 Z= 0.318 Chirality : 0.041 0.147 1426 Planarity : 0.005 0.053 1564 Dihedral : 6.061 51.672 1288 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.42 % Allowed : 20.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1110 helix: 1.30 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.74 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 813 TYR 0.025 0.001 TYR B 477 PHE 0.023 0.001 PHE A 462 TRP 0.023 0.001 TRP A 650 HIS 0.006 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9372) covalent geometry : angle 0.61341 / 0.32 (12734) SS BOND : bond 0.00181 / 0.12 ( 10) SS BOND : angle 0.92754 / 0.69 ( 20) hydrogen bonds : bond 0.04535 / 3.25 ( 592) hydrogen bonds : angle 4.62401 / 3.29 ( 1758) Misc. bond : bond 0.00011 / 0.01 ( 2) *********************** 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 173 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.250 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: 0.8373 (OUTLIER) cc_final: 0.7986 (tt) REVERT: A 373 ILE cc_start: 0.8368 (mt) cc_final: 0.8043 (mt) REVERT: A 477 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.6300 (p90) REVERT: B 322 LEU cc_start: 0.8399 (mm) cc_final: 0.7956 (tt) REVERT: B 373 ILE cc_start: 0.8306 (mt) cc_final: 0.7952 (mt) REVERT: B 553 MET cc_start: 0.8163 (tpp) cc_final: 0.7810 (tpp) REVERT: B 821 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6347 (pm20) outliers start: 22 outliers final: 13 residues processed: 167 average time/residue: 0.0738 time to fit residues: 18.6218 Evaluate side-chains 163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 814 ASN Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 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 = 0.4002 r_free = 0.4002 target = 0.143210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.122068 restraints weight = 18714.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.124366 restraints weight = 11760.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.125410 restraints weight = 8747.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126714 restraints weight = 7459.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.127419 restraints weight = 6495.740| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9384 Z= 0.138 Angle : 0.615 11.688 12754 Z= 0.317 Chirality : 0.041 0.146 1426 Planarity : 0.005 0.054 1564 Dihedral : 5.991 51.072 1288 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.87 % Allowed : 20.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1110 helix: 1.34 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.71 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 753 TYR 0.023 0.001 TYR B 477 PHE 0.023 0.001 PHE A 462 TRP 0.023 0.001 TRP A 650 HIS 0.004 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 9372) covalent geometry : angle 0.61490 / 0.32 (12734) SS BOND : bond 0.00176 / 0.11 ( 10) SS BOND : angle 0.91276 / 0.68 ( 20) hydrogen bonds : bond 0.04465 / 3.20 ( 592) hydrogen bonds : angle 4.58619 / 3.26 ( 1758) Misc. bond : bond 0.00018 / 0.01 ( 2) ********************** 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 172 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.361 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: 0.8363 (OUTLIER) cc_final: 0.7993 (tt) REVERT: A 373 ILE cc_start: 0.8365 (mt) cc_final: 0.8038 (mt) REVERT: A 477 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.6241 (p90) REVERT: A 553 MET cc_start: 0.8146 (tpp) cc_final: 0.7810 (tpp) REVERT: B 322 LEU cc_start: 0.8342 (mm) cc_final: 0.7912 (tt) REVERT: B 373 ILE cc_start: 0.8296 (mt) cc_final: 0.7950 (mt) REVERT: B 386 MET cc_start: 0.7629 (tpt) cc_final: 0.7330 (tpt) REVERT: B 530 LYS cc_start: 0.7679 (mmtt) cc_final: 0.6431 (ttpt) REVERT: B 553 MET cc_start: 0.8137 (tpp) cc_final: 0.7803 (tpp) REVERT: B 565 SER cc_start: 0.8763 (m) cc_final: 0.8515 (t) REVERT: B 812 PHE cc_start: 0.7964 (m-80) cc_final: 0.7753 (m-80) REVERT: B 821 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6401 (pm20) outliers start: 17 outliers final: 13 residues processed: 169 average time/residue: 0.0766 time to fit residues: 19.1874 Evaluate side-chains 167 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU 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 814 ASN Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN ** B 814 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 = 0.3994 r_free = 0.3994 target = 0.142761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.121823 restraints weight = 18599.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.124025 restraints weight = 11926.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.125263 restraints weight = 8967.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126310 restraints weight = 7583.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.126539 restraints weight = 6690.285| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9384 Z= 0.153 Angle : 0.630 11.024 12754 Z= 0.322 Chirality : 0.041 0.140 1426 Planarity : 0.005 0.055 1564 Dihedral : 5.959 50.707 1288 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.98 % Allowed : 20.93 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.24), residues: 1110 helix: 1.37 (0.18), residues: 772 sheet: None (None), residues: 0 loop : -0.70 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 813 TYR 0.023 0.001 TYR B 477 PHE 0.025 0.002 PHE A 462 TRP 0.023 0.001 TRP A 650 HIS 0.004 0.001 HIS B 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 9372) covalent geometry : angle 0.62918 / 0.32 (12734) SS BOND : bond 0.00208 / 0.13 ( 10) SS BOND : angle 0.93369 / 0.69 ( 20) hydrogen bonds : bond 0.04503 / 3.23 ( 592) hydrogen bonds : angle 4.60007 / 3.28 ( 1758) Misc. bond : bond 0.00013 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.44 seconds wall clock time: 26 minutes 25.16 seconds (1585.16 seconds total)