Starting phenix.real_space_refine on Fri Jul 3 03:54:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1p_70015/07_2026/9o1p_70015_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1p_70015/07_2026/9o1p_70015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o1p_70015/07_2026/9o1p_70015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1p_70015/07_2026/9o1p_70015.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1p_70015/07_2026/9o1p_70015_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1p_70015/07_2026/9o1p_70015_neut.cif" } resolution = 3.48 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= 0.002 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 78 5.16 5 C 7730 2.51 5 N 1866 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11714 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5854 Classifications: {'peptide': 716} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 32, 'TRANS': 683} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 5.81, per 1000 atoms: 0.50 Number of scatterers: 11714 At special positions: 0 Unit cell: (109.725, 109.725, 113.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 78 16.00 O 2034 8.00 N 1866 7.00 C 7730 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 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=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 612.9 milliseconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 8 sheets defined 65.8% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.728A pdb=" N ILE A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 4.270A pdb=" N PHE A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.792A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 293 through 328 removed outlier: 3.543A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.969A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.840A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 Processing helix chain 'A' and resid 458 through 487 removed outlier: 3.706A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 539 removed outlier: 4.652A pdb=" N ILE A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 3.952A pdb=" N MET A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 removed outlier: 4.238A pdb=" N VAL A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 removed outlier: 3.559A pdb=" N HIS A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 removed outlier: 4.108A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 685 Processing helix chain 'A' and resid 687 through 710 removed outlier: 3.651A pdb=" N ASN A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.741A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 759 removed outlier: 3.560A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.529A pdb=" N TYR A 855 " --> pdb=" O PHE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 881 removed outlier: 4.352A pdb=" N SER A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 109 Processing helix chain 'B' and resid 131 through 141 removed outlier: 3.729A pdb=" N ILE B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 4.270A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.791A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 328 removed outlier: 3.543A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 364 through 375 removed outlier: 3.969A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.840A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 Processing helix chain 'B' and resid 458 through 487 removed outlier: 3.706A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 539 removed outlier: 4.652A pdb=" N ILE B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 3.952A pdb=" N MET B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 removed outlier: 4.238A pdb=" N VAL B 625 " --> pdb=" O ASN B 621 " (cutoff:3.500A) Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.559A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 4.109A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 710 removed outlier: 3.651A pdb=" N ASN B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.741A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 759 removed outlier: 3.561A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.528A pdb=" N TYR B 855 " --> pdb=" O PHE B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 881 removed outlier: 4.351A pdb=" N SER B 866 " --> pdb=" O LYS B 862 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 113 removed outlier: 3.539A pdb=" N PHE A 73 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149 removed outlier: 7.044A pdb=" N PHE A 183 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA4, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.539A pdb=" N PHE B 73 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 149 removed outlier: 7.045A pdb=" N PHE B 183 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA8, first strand: chain 'B' and resid 784 through 785 688 hydrogen bonds defined for protein. 2022 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: 1.91 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3535 1.34 - 1.46: 3184 1.46 - 1.58: 5197 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 12036 Sorted by residual: bond pdb=" N PRO B 357 " pdb=" CD PRO B 357 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.14e+01 bond pdb=" N PRO A 357 " pdb=" CD PRO A 357 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.11e+01 bond pdb=" CA GLY B 723 " pdb=" C GLY B 723 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.19e-02 7.06e+03 1.82e+00 bond pdb=" CA GLY A 723 " pdb=" C GLY A 723 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.19e-02 7.06e+03 1.76e+00 bond pdb=" C TYR B 270 " pdb=" N ARG B 271 " ideal model delta sigma weight residual 1.333 1.316 0.016 1.45e-02 4.76e+03 1.28e+00 ... (remaining 12031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 16125 2.56 - 5.13: 181 5.13 - 7.69: 16 7.69 - 10.25: 2 10.25 - 12.82: 2 Bond angle restraints: 16326 Sorted by residual: angle pdb=" C CYS B 356 " pdb=" N PRO B 357 " pdb=" CA PRO B 357 " ideal model delta sigma weight residual 119.84 125.50 -5.66 1.25e+00 6.40e-01 2.05e+01 angle pdb=" C CYS A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta sigma weight residual 119.84 125.43 -5.59 1.25e+00 6.40e-01 2.00e+01 angle pdb=" C ARG A 701 " pdb=" N VAL A 702 " pdb=" CA VAL A 702 " ideal model delta sigma weight residual 122.35 118.25 4.10 1.18e+00 7.18e-01 1.21e+01 angle pdb=" C ARG B 701 " pdb=" N VAL B 702 " pdb=" CA VAL B 702 " ideal model delta sigma weight residual 122.35 118.27 4.08 1.18e+00 7.18e-01 1.20e+01 angle pdb=" C ILE A 762 " pdb=" CA ILE A 762 " pdb=" CB ILE A 762 " ideal model delta sigma weight residual 110.88 114.17 -3.29 9.80e-01 1.04e+00 1.12e+01 ... (remaining 16321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6231 17.89 - 35.78: 693 35.78 - 53.67: 128 53.67 - 71.55: 14 71.55 - 89.44: 12 Dihedral angle restraints: 7078 sinusoidal: 2844 harmonic: 4234 Sorted by residual: dihedral pdb=" CB CYS B 349 " pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual 93.00 13.82 79.18 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS A 349 " pdb=" SG CYS A 349 " pdb=" SG CYS A 807 " pdb=" CB CYS A 807 " ideal model delta sinusoidal sigma weight residual 93.00 13.83 79.17 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 372 " pdb=" CB CYS B 372 " ideal model delta sinusoidal sigma weight residual -86.00 -149.60 63.60 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 7075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1049 0.030 - 0.060: 529 0.060 - 0.090: 141 0.090 - 0.120: 62 0.120 - 0.150: 11 Chirality restraints: 1792 Sorted by residual: chirality pdb=" CA PHE B 253 " pdb=" N PHE B 253 " pdb=" C PHE B 253 " pdb=" CB PHE B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA PHE A 253 " pdb=" N PHE A 253 " pdb=" C PHE A 253 " pdb=" CB PHE A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA ASN A 254 " pdb=" N ASN A 254 " pdb=" C ASN A 254 " pdb=" CB ASN A 254 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1789 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 356 " 0.062 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO A 357 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 357 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 357 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 356 " -0.062 5.00e-02 4.00e+02 9.67e-02 1.49e+01 pdb=" N PRO B 357 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 357 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 357 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 762 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO B 763 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 763 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 763 " -0.026 5.00e-02 4.00e+02 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2136 2.76 - 3.29: 11847 3.29 - 3.83: 19905 3.83 - 4.36: 21705 4.36 - 4.90: 37910 Nonbonded interactions: 93503 Sorted by model distance: nonbonded pdb=" O LEU B 217 " pdb=" OH TYR B 222 " model vdw 2.224 3.040 nonbonded pdb=" O LEU A 217 " pdb=" OH TYR A 222 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASN A 621 " pdb="CA CA A1001 " model vdw 2.241 3.250 nonbonded pdb=" OD1 ASN B 621 " pdb="CA CA B1001 " model vdw 2.241 3.250 nonbonded pdb=" OD1 ASP A 859 " pdb="CA CA A1003 " model vdw 2.242 3.250 ... (remaining 93498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.110 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12046 Z= 0.178 Angle : 0.682 12.817 16346 Z= 0.391 Chirality : 0.040 0.150 1792 Planarity : 0.005 0.097 2016 Dihedral : 14.980 89.443 4320 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % Rotamer: Outliers : 0.24 % Allowed : 17.51 % Favored : 82.25 % 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: 0.80 (0.23), residues: 1400 helix: 1.16 (0.18), residues: 830 sheet: 0.20 (0.57), residues: 98 loop : -0.41 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.013 0.001 TYR A 255 PHE 0.028 0.002 PHE B 253 TRP 0.014 0.001 TRP B 273 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (12036) covalent geometry : angle 0.68010 / 0.39 (16326) SS BOND : bond 0.00227 / 0.15 ( 10) SS BOND : angle 1.45976 / 0.75 ( 20) hydrogen bonds : bond 0.15756 / 10.24 ( 688) hydrogen bonds : angle 6.75009 / 4.86 ( 2022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.438 Fit side-chains REVERT: A 573 PHE cc_start: 0.7848 (t80) cc_final: 0.7629 (t80) REVERT: A 742 MET cc_start: 0.7202 (mtt) cc_final: 0.6719 (mtm) outliers start: 3 outliers final: 2 residues processed: 168 average time/residue: 0.0836 time to fit residues: 22.0301 Evaluate side-chains 154 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain B residue 807 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 HIS A 351 GLN A 608 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS B 351 GLN B 608 GLN B 652 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.186715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126555 restraints weight = 15295.708| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.77 r_work: 0.3315 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12046 Z= 0.121 Angle : 0.539 7.545 16346 Z= 0.283 Chirality : 0.039 0.146 1792 Planarity : 0.006 0.076 2016 Dihedral : 4.144 22.279 1568 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.41 % Allowed : 13.79 % Favored : 82.81 % 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: 1.40 (0.23), residues: 1400 helix: 1.75 (0.18), residues: 838 sheet: -0.12 (0.55), residues: 98 loop : -0.28 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 252 TYR 0.012 0.001 TYR B 406 PHE 0.016 0.001 PHE A 253 TRP 0.014 0.001 TRP B 273 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (12036) covalent geometry : angle 0.53702 / 0.28 (16326) SS BOND : bond 0.00141 / 0.08 ( 10) SS BOND : angle 1.52780 / 0.76 ( 20) hydrogen bonds : bond 0.04013 / 2.60 ( 688) hydrogen bonds : angle 4.51909 / 3.19 ( 2022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.440 Fit side-chains REVERT: A 126 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8083 (m) REVERT: A 573 PHE cc_start: 0.8154 (t80) cc_final: 0.7921 (t80) REVERT: A 671 MET cc_start: 0.8879 (mmt) cc_final: 0.8539 (mmt) REVERT: A 691 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8310 (tt) REVERT: B 671 MET cc_start: 0.8801 (mmt) cc_final: 0.8487 (mmt) REVERT: B 691 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8302 (tt) outliers start: 43 outliers final: 22 residues processed: 184 average time/residue: 0.0811 time to fit residues: 23.9066 Evaluate side-chains 169 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 chunk 82 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN A 652 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.180404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.120092 restraints weight = 15712.875| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.90 r_work: 0.3212 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12046 Z= 0.248 Angle : 0.602 7.758 16346 Z= 0.319 Chirality : 0.042 0.148 1792 Planarity : 0.006 0.079 2016 Dihedral : 4.265 22.873 1566 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.28 % Allowed : 15.37 % Favored : 80.35 % 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: 1.08 (0.22), residues: 1400 helix: 1.46 (0.18), residues: 846 sheet: -0.18 (0.54), residues: 98 loop : -0.40 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 211 TYR 0.014 0.001 TYR A 138 PHE 0.017 0.002 PHE B 560 TRP 0.013 0.002 TRP B 389 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (12036) covalent geometry : angle 0.60041 / 0.32 (16326) SS BOND : bond 0.00327 / 0.20 ( 10) SS BOND : angle 1.43585 / 0.79 ( 20) hydrogen bonds : bond 0.04465 / 2.92 ( 688) hydrogen bonds : angle 4.51497 / 3.18 ( 2022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.8687 (tpp) cc_final: 0.8485 (mmt) REVERT: A 573 PHE cc_start: 0.8245 (t80) cc_final: 0.7994 (t80) REVERT: A 691 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 711 PHE cc_start: 0.8607 (m-80) cc_final: 0.8361 (m-80) REVERT: B 691 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8381 (tt) REVERT: B 711 PHE cc_start: 0.8590 (m-80) cc_final: 0.8352 (m-80) REVERT: B 842 MET cc_start: 0.8753 (ttp) cc_final: 0.8474 (ttt) outliers start: 54 outliers final: 36 residues processed: 206 average time/residue: 0.0776 time to fit residues: 25.2408 Evaluate side-chains 197 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.184866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119330 restraints weight = 15938.994| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.79 r_work: 0.3333 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12046 Z= 0.123 Angle : 0.515 6.798 16346 Z= 0.272 Chirality : 0.039 0.148 1792 Planarity : 0.005 0.072 2016 Dihedral : 4.075 21.316 1566 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.33 % Allowed : 17.67 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.31 (0.22), residues: 1400 helix: 1.72 (0.18), residues: 844 sheet: -0.55 (0.57), residues: 80 loop : -0.36 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 252 TYR 0.014 0.001 TYR B 138 PHE 0.016 0.001 PHE A 183 TRP 0.014 0.001 TRP B 397 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12036) covalent geometry : angle 0.51436 / 0.27 (16326) SS BOND : bond 0.00175 / 0.11 ( 10) SS BOND : angle 0.99870 / 0.55 ( 20) hydrogen bonds : bond 0.03777 / 2.46 ( 688) hydrogen bonds : angle 4.27868 / 3.00 ( 2022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.444 Fit side-chains REVERT: A 126 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8173 (m) REVERT: A 573 PHE cc_start: 0.8210 (t80) cc_final: 0.7959 (t80) REVERT: A 691 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8456 (tt) REVERT: A 711 PHE cc_start: 0.8552 (m-80) cc_final: 0.8328 (m-80) REVERT: A 786 ILE cc_start: 0.8902 (pt) cc_final: 0.8648 (mt) REVERT: B 126 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8125 (m) REVERT: B 659 MET cc_start: 0.8256 (mmm) cc_final: 0.7824 (mmm) REVERT: B 691 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8378 (tt) REVERT: B 786 ILE cc_start: 0.8910 (pt) cc_final: 0.8658 (mt) REVERT: B 842 MET cc_start: 0.8753 (ttp) cc_final: 0.8428 (ttt) outliers start: 42 outliers final: 29 residues processed: 197 average time/residue: 0.0801 time to fit residues: 24.9485 Evaluate side-chains 187 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 807 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.180173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118016 restraints weight = 16133.170| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.49 r_work: 0.3220 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12046 Z= 0.289 Angle : 0.624 8.140 16346 Z= 0.331 Chirality : 0.043 0.155 1792 Planarity : 0.006 0.071 2016 Dihedral : 4.377 24.614 1566 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.88 % Allowed : 18.15 % Favored : 77.97 % 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: 0.92 (0.22), residues: 1400 helix: 1.39 (0.18), residues: 846 sheet: -0.50 (0.58), residues: 80 loop : -0.52 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 252 TYR 0.012 0.001 TYR A 138 PHE 0.019 0.002 PHE A 560 TRP 0.015 0.002 TRP B 389 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.29 (12036) covalent geometry : angle 0.62141 / 0.33 (16326) SS BOND : bond 0.00535 / 0.27 ( 10) SS BOND : angle 1.71256 / 0.90 ( 20) hydrogen bonds : bond 0.04435 / 2.91 ( 688) hydrogen bonds : angle 4.45409 / 3.13 ( 2022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.8347 (t80) cc_final: 0.8089 (t80) REVERT: A 652 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7922 (pp30) REVERT: A 691 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 711 PHE cc_start: 0.8836 (m-80) cc_final: 0.8472 (m-80) REVERT: A 786 ILE cc_start: 0.8951 (pt) cc_final: 0.8690 (mt) REVERT: B 671 MET cc_start: 0.9060 (mmm) cc_final: 0.8787 (mmt) REVERT: B 691 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8413 (tt) REVERT: B 786 ILE cc_start: 0.8936 (pt) cc_final: 0.8679 (mt) REVERT: B 842 MET cc_start: 0.8795 (ttp) cc_final: 0.8556 (ttt) outliers start: 49 outliers final: 40 residues processed: 204 average time/residue: 0.0734 time to fit residues: 23.6320 Evaluate side-chains 201 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 30.0000 chunk 93 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.184636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123474 restraints weight = 16004.268| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.36 r_work: 0.3310 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.035 12046 Z= 0.121 Angle : 0.524 7.802 16346 Z= 0.276 Chirality : 0.039 0.151 1792 Planarity : 0.005 0.066 2016 Dihedral : 4.110 21.981 1566 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.33 % Allowed : 19.02 % Favored : 77.65 % 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: 1.31 (0.22), residues: 1400 helix: 1.72 (0.18), residues: 844 sheet: -0.39 (0.58), residues: 80 loop : -0.40 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 252 TYR 0.013 0.001 TYR A 580 PHE 0.019 0.001 PHE A 183 TRP 0.016 0.001 TRP A 397 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (12036) covalent geometry : angle 0.52260 / 0.28 (16326) SS BOND : bond 0.00133 / 0.08 ( 10) SS BOND : angle 1.10395 / 0.58 ( 20) hydrogen bonds : bond 0.03726 / 2.43 ( 688) hydrogen bonds : angle 4.25558 / 2.98 ( 2022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.8261 (t80) cc_final: 0.7990 (t80) REVERT: A 691 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8516 (tt) REVERT: A 711 PHE cc_start: 0.8725 (m-80) cc_final: 0.8404 (m-80) REVERT: A 786 ILE cc_start: 0.8955 (pt) cc_final: 0.8693 (mt) REVERT: B 659 MET cc_start: 0.8325 (mmm) cc_final: 0.8062 (mmm) REVERT: B 671 MET cc_start: 0.8944 (mmm) cc_final: 0.8659 (mmm) REVERT: B 691 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8420 (tt) REVERT: B 711 PHE cc_start: 0.8530 (m-80) cc_final: 0.8257 (m-80) REVERT: B 786 ILE cc_start: 0.8904 (pt) cc_final: 0.8655 (mt) REVERT: B 842 MET cc_start: 0.8703 (ttp) cc_final: 0.8425 (ttt) outliers start: 42 outliers final: 29 residues processed: 198 average time/residue: 0.0756 time to fit residues: 23.6793 Evaluate side-chains 183 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 807 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 65 optimal weight: 0.0270 chunk 137 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.182078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119028 restraints weight = 15915.245| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.35 r_work: 0.3260 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12046 Z= 0.173 Angle : 0.557 9.162 16346 Z= 0.292 Chirality : 0.040 0.152 1792 Planarity : 0.005 0.066 2016 Dihedral : 4.126 22.854 1566 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.65 % Allowed : 18.86 % Favored : 77.50 % 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: 1.26 (0.22), residues: 1400 helix: 1.66 (0.18), residues: 846 sheet: -0.24 (0.59), residues: 80 loop : -0.40 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.012 0.001 TYR A 138 PHE 0.019 0.001 PHE B 183 TRP 0.012 0.001 TRP A 397 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (12036) covalent geometry : angle 0.55605 / 0.29 (16326) SS BOND : bond 0.00225 / 0.14 ( 10) SS BOND : angle 1.24919 / 0.68 ( 20) hydrogen bonds : bond 0.03887 / 2.54 ( 688) hydrogen bonds : angle 4.25975 / 2.98 ( 2022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8310 (p0) REVERT: A 573 PHE cc_start: 0.8282 (t80) cc_final: 0.8047 (t80) REVERT: A 608 GLN cc_start: 0.8697 (tp40) cc_final: 0.8423 (tp40) REVERT: A 671 MET cc_start: 0.9029 (mmm) cc_final: 0.8641 (mmm) REVERT: A 691 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8478 (tt) REVERT: A 711 PHE cc_start: 0.8782 (m-80) cc_final: 0.8499 (m-80) REVERT: A 786 ILE cc_start: 0.8970 (pt) cc_final: 0.8718 (mt) REVERT: A 842 MET cc_start: 0.8894 (ttp) cc_final: 0.8668 (ttt) REVERT: B 573 PHE cc_start: 0.8338 (t80) cc_final: 0.8129 (t80) REVERT: B 588 LEU cc_start: 0.8395 (pt) cc_final: 0.8194 (mm) REVERT: B 691 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8400 (tt) REVERT: B 711 PHE cc_start: 0.8589 (m-80) cc_final: 0.8333 (m-80) REVERT: B 786 ILE cc_start: 0.8981 (pt) cc_final: 0.8734 (mt) REVERT: B 842 MET cc_start: 0.8685 (ttp) cc_final: 0.8452 (ttt) outliers start: 46 outliers final: 37 residues processed: 192 average time/residue: 0.0689 time to fit residues: 21.1992 Evaluate side-chains 194 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 807 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 9 optimal weight: 0.0040 chunk 38 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 40.0000 chunk 53 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.185891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120261 restraints weight = 15789.217| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.78 r_work: 0.3341 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12046 Z= 0.110 Angle : 0.537 9.515 16346 Z= 0.276 Chirality : 0.038 0.150 1792 Planarity : 0.005 0.064 2016 Dihedral : 3.998 21.217 1566 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.01 % Allowed : 19.49 % Favored : 77.50 % 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: 1.42 (0.23), residues: 1400 helix: 1.79 (0.18), residues: 848 sheet: 0.12 (0.63), residues: 70 loop : -0.42 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.013 0.001 TYR A 580 PHE 0.022 0.001 PHE B 183 TRP 0.015 0.001 TRP A 397 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (12036) covalent geometry : angle 0.53645 / 0.28 (16326) SS BOND : bond 0.00153 / 0.09 ( 10) SS BOND : angle 0.98863 / 0.54 ( 20) hydrogen bonds : bond 0.03543 / 2.32 ( 688) hydrogen bonds : angle 4.16118 / 2.91 ( 2022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.8248 (t80) cc_final: 0.8032 (t80) REVERT: A 608 GLN cc_start: 0.8649 (tp40) cc_final: 0.8379 (tp40) REVERT: A 691 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8438 (tt) REVERT: A 711 PHE cc_start: 0.8663 (m-80) cc_final: 0.8379 (m-80) REVERT: A 786 ILE cc_start: 0.8944 (pt) cc_final: 0.8699 (mt) REVERT: A 842 MET cc_start: 0.8829 (ttp) cc_final: 0.8591 (ttt) REVERT: B 573 PHE cc_start: 0.8237 (t80) cc_final: 0.8002 (t80) REVERT: B 659 MET cc_start: 0.8228 (mmm) cc_final: 0.7931 (mmm) REVERT: B 711 PHE cc_start: 0.8503 (m-80) cc_final: 0.8255 (m-80) REVERT: B 842 MET cc_start: 0.8615 (ttp) cc_final: 0.8383 (ttt) outliers start: 38 outliers final: 30 residues processed: 198 average time/residue: 0.0646 time to fit residues: 20.8495 Evaluate side-chains 188 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 807 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 103 optimal weight: 0.0030 chunk 25 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** 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 = 0.4228 r_free = 0.4228 target = 0.183352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119901 restraints weight = 15807.046| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.39 r_work: 0.3275 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12046 Z= 0.158 Angle : 0.568 8.999 16346 Z= 0.291 Chirality : 0.040 0.151 1792 Planarity : 0.005 0.065 2016 Dihedral : 4.034 22.173 1566 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.54 % Allowed : 20.29 % Favored : 77.18 % 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: 1.39 (0.23), residues: 1400 helix: 1.74 (0.18), residues: 850 sheet: 0.24 (0.62), residues: 70 loop : -0.40 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.012 0.001 TYR A 580 PHE 0.020 0.001 PHE A 665 TRP 0.011 0.002 TRP A 397 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (12036) covalent geometry : angle 0.56697 / 0.29 (16326) SS BOND : bond 0.00223 / 0.13 ( 10) SS BOND : angle 1.21708 / 0.67 ( 20) hydrogen bonds : bond 0.03745 / 2.45 ( 688) hydrogen bonds : angle 4.18779 / 2.93 ( 2022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.8276 (t80) cc_final: 0.8054 (t80) REVERT: A 671 MET cc_start: 0.9020 (mmm) cc_final: 0.8656 (mmm) REVERT: A 691 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8494 (tt) REVERT: A 711 PHE cc_start: 0.8763 (m-80) cc_final: 0.8332 (m-80) REVERT: A 786 ILE cc_start: 0.8978 (pt) cc_final: 0.8737 (mt) REVERT: A 842 MET cc_start: 0.8870 (ttp) cc_final: 0.8648 (ttt) REVERT: B 573 PHE cc_start: 0.8289 (t80) cc_final: 0.8080 (t80) REVERT: B 588 LEU cc_start: 0.8412 (pt) cc_final: 0.8211 (mm) REVERT: B 659 MET cc_start: 0.8229 (mmm) cc_final: 0.7894 (mmm) REVERT: B 691 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8395 (tt) REVERT: B 711 PHE cc_start: 0.8655 (m-80) cc_final: 0.8382 (m-80) REVERT: B 786 ILE cc_start: 0.8932 (pt) cc_final: 0.8686 (mt) REVERT: B 842 MET cc_start: 0.8674 (ttp) cc_final: 0.8445 (ttt) outliers start: 32 outliers final: 28 residues processed: 189 average time/residue: 0.0709 time to fit residues: 21.6439 Evaluate side-chains 188 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 807 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 0.0060 chunk 72 optimal weight: 0.0050 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** 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 = 0.4257 r_free = 0.4257 target = 0.186447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120920 restraints weight = 15996.137| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.80 r_work: 0.3348 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12046 Z= 0.110 Angle : 0.550 9.366 16346 Z= 0.281 Chirality : 0.038 0.148 1792 Planarity : 0.005 0.062 2016 Dihedral : 3.943 20.442 1566 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.22 % Allowed : 21.08 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.47 (0.23), residues: 1400 helix: 1.82 (0.18), residues: 848 sheet: 0.21 (0.62), residues: 70 loop : -0.38 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.013 0.001 TYR A 580 PHE 0.021 0.001 PHE B 183 TRP 0.016 0.001 TRP A 397 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (12036) covalent geometry : angle 0.54891 / 0.28 (16326) SS BOND : bond 0.00153 / 0.09 ( 10) SS BOND : angle 0.99692 / 0.55 ( 20) hydrogen bonds : bond 0.03461 / 2.27 ( 688) hydrogen bonds : angle 4.15771 / 2.90 ( 2022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 CYS cc_start: 0.7710 (m) cc_final: 0.7266 (p) REVERT: A 573 PHE cc_start: 0.8255 (t80) cc_final: 0.8036 (t80) REVERT: A 659 MET cc_start: 0.8350 (mmm) cc_final: 0.8004 (mmm) REVERT: A 711 PHE cc_start: 0.8572 (m-80) cc_final: 0.8302 (m-80) REVERT: A 786 ILE cc_start: 0.8969 (pt) cc_final: 0.8724 (mt) REVERT: A 842 MET cc_start: 0.8816 (ttp) cc_final: 0.8587 (ttt) REVERT: B 573 PHE cc_start: 0.8229 (t80) cc_final: 0.8028 (t80) REVERT: B 588 LEU cc_start: 0.8355 (pt) cc_final: 0.8136 (mm) REVERT: B 659 MET cc_start: 0.8214 (mmm) cc_final: 0.7904 (mmm) REVERT: B 711 PHE cc_start: 0.8600 (m-80) cc_final: 0.8372 (m-80) REVERT: B 842 MET cc_start: 0.8599 (ttp) cc_final: 0.8378 (ttt) outliers start: 28 outliers final: 28 residues processed: 190 average time/residue: 0.0685 time to fit residues: 20.8206 Evaluate side-chains 189 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 596 CYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 807 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** 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 = 0.4225 r_free = 0.4225 target = 0.182940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118918 restraints weight = 16006.163| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.22 r_work: 0.3280 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12046 Z= 0.168 Angle : 0.579 8.987 16346 Z= 0.297 Chirality : 0.040 0.165 1792 Planarity : 0.005 0.062 2016 Dihedral : 4.028 22.373 1566 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.77 % Allowed : 20.92 % Favored : 76.31 % 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: 1.35 (0.23), residues: 1400 helix: 1.71 (0.18), residues: 850 sheet: 0.18 (0.63), residues: 70 loop : -0.41 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 252 TYR 0.012 0.001 TYR B 138 PHE 0.020 0.002 PHE A 665 TRP 0.010 0.001 TRP A 273 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (12036) covalent geometry : angle 0.57823 / 0.30 (16326) SS BOND : bond 0.00241 / 0.15 ( 10) SS BOND : angle 1.23773 / 0.69 ( 20) hydrogen bonds : bond 0.03766 / 2.45 ( 688) hydrogen bonds : angle 4.18540 / 2.93 ( 2022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.69 seconds wall clock time: 42 minutes 0.85 seconds (2520.85 seconds total)