Starting phenix.real_space_refine on Thu Jun 4 09:00:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o1p_70015/06_2026/9o1p_70015_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o1p_70015/06_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_70015/06_2026/9o1p_70015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o1p_70015/06_2026/9o1p_70015.map" model { file = "/net/cci-nas-00/data/ceres_data/9o1p_70015/06_2026/9o1p_70015_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o1p_70015/06_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-6079/lib/python3.9/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, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 5.06, per 1000 atoms: 0.43 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: 0.89 Conformation dependent library (CDL) restraints added in 474.4 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: 0.34 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: 1.97 Time building geometry restraints manager: 1.19 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 2.510 nonbonded pdb=" OD1 ASN B 621 " pdb="CA CA B1001 " model vdw 2.241 2.510 nonbonded pdb=" OD1 ASP A 859 " pdb="CA CA A1003 " model vdw 2.242 2.510 ... (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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.610 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.402 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: 0.0877 time to fit residues: 22.9413 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 : 0.482 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** B 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.186964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126584 restraints weight = 15356.171| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.76 r_work: 0.3312 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12046 Z= 0.122 Angle : 0.536 7.372 16346 Z= 0.282 Chirality : 0.039 0.143 1792 Planarity : 0.006 0.076 2016 Dihedral : 4.129 22.050 1568 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.49 % Allowed : 13.71 % 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: 1.39 (0.23), residues: 1400 helix: 1.74 (0.18), residues: 838 sheet: -0.13 (0.55), residues: 98 loop : -0.28 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 252 TYR 0.013 0.001 TYR B 406 PHE 0.016 0.001 PHE A 253 TRP 0.013 0.001 TRP B 273 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12036) covalent geometry : angle 0.53416 / 0.28 (16326) SS BOND : bond 0.00142 / 0.08 ( 10) SS BOND : angle 1.47328 / 0.73 ( 20) hydrogen bonds : bond 0.03996 / 2.60 ( 688) hydrogen bonds : angle 4.48519 / 3.17 ( 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 199 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.474 Fit side-chains REVERT: A 126 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8092 (m) REVERT: A 573 PHE cc_start: 0.8160 (t80) cc_final: 0.7933 (t80) REVERT: A 691 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8298 (tt) REVERT: A 742 MET cc_start: 0.8216 (mtt) cc_final: 0.7705 (mtm) REVERT: B 691 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8304 (tt) outliers start: 44 outliers final: 24 residues processed: 187 average time/residue: 0.0823 time to fit residues: 24.6644 Evaluate side-chains 170 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 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 875 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 9 optimal weight: 0.0970 chunk 14 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 50.0000 chunk 82 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4218 r_free = 0.4218 target = 0.183589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.123763 restraints weight = 15672.710| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.89 r_work: 0.3258 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12046 Z= 0.174 Angle : 0.543 7.701 16346 Z= 0.286 Chirality : 0.040 0.148 1792 Planarity : 0.006 0.075 2016 Dihedral : 4.048 21.019 1566 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.12 % Allowed : 15.53 % 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: 1.33 (0.22), residues: 1400 helix: 1.69 (0.18), residues: 844 sheet: -0.17 (0.54), residues: 98 loop : -0.33 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 252 TYR 0.014 0.001 TYR A 138 PHE 0.015 0.001 PHE A 560 TRP 0.011 0.002 TRP A 273 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (12036) covalent geometry : angle 0.54140 / 0.29 (16326) SS BOND : bond 0.00411 / 0.20 ( 10) SS BOND : angle 1.18772 / 0.65 ( 20) hydrogen bonds : bond 0.04066 / 2.65 ( 688) hydrogen bonds : angle 4.35206 / 3.06 ( 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 216 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.8204 (t80) cc_final: 0.7956 (t80) REVERT: A 691 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8324 (tt) REVERT: A 711 PHE cc_start: 0.8551 (m-80) cc_final: 0.8310 (m-80) REVERT: B 691 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8335 (tt) REVERT: B 711 PHE cc_start: 0.8505 (m-80) cc_final: 0.8277 (m-80) REVERT: B 842 MET cc_start: 0.8717 (ttp) cc_final: 0.8336 (ttt) outliers start: 52 outliers final: 33 residues processed: 199 average time/residue: 0.0854 time to fit residues: 26.8901 Evaluate side-chains 184 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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 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 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 279 ILE 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 625 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 691 LEU 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: 10.0000 chunk 32 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4222 r_free = 0.4222 target = 0.183055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122688 restraints weight = 15991.091| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.97 r_work: 0.3269 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12046 Z= 0.177 Angle : 0.540 7.989 16346 Z= 0.285 Chirality : 0.040 0.151 1792 Planarity : 0.005 0.072 2016 Dihedral : 4.072 22.150 1566 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.88 % Allowed : 17.19 % Favored : 78.92 % 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: 1.30 (0.22), residues: 1400 helix: 1.67 (0.18), residues: 846 sheet: -0.13 (0.54), residues: 98 loop : -0.38 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 289 TYR 0.012 0.001 TYR A 406 PHE 0.015 0.001 PHE B 560 TRP 0.011 0.001 TRP A 273 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (12036) covalent geometry : angle 0.53890 / 0.28 (16326) SS BOND : bond 0.00219 / 0.14 ( 10) SS BOND : angle 1.19707 / 0.67 ( 20) hydrogen bonds : bond 0.03995 / 2.61 ( 688) hydrogen bonds : angle 4.28864 / 3.01 ( 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 205 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8112 (m) REVERT: A 573 PHE cc_start: 0.8208 (t80) cc_final: 0.7941 (t80) REVERT: A 671 MET cc_start: 0.9053 (mmm) cc_final: 0.8753 (mmm) REVERT: A 691 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A 711 PHE cc_start: 0.8576 (m-80) cc_final: 0.8339 (m-80) REVERT: B 671 MET cc_start: 0.9031 (mmm) cc_final: 0.8722 (mmm) REVERT: B 691 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 711 PHE cc_start: 0.8494 (m-80) cc_final: 0.8268 (m-80) REVERT: B 842 MET cc_start: 0.8775 (ttp) cc_final: 0.8436 (ttt) outliers start: 49 outliers final: 34 residues processed: 192 average time/residue: 0.0866 time to fit residues: 26.4228 Evaluate side-chains 185 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 612 ILE 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 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 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 578 VAL Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 596 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 32 optimal weight: 0.0170 chunk 88 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4225 r_free = 0.4225 target = 0.183445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123198 restraints weight = 16007.479| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.96 r_work: 0.3271 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12046 Z= 0.159 Angle : 0.530 8.227 16346 Z= 0.280 Chirality : 0.040 0.152 1792 Planarity : 0.005 0.068 2016 Dihedral : 4.093 22.182 1566 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.96 % Allowed : 17.59 % Favored : 78.45 % 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: 1.30 (0.22), residues: 1400 helix: 1.72 (0.18), residues: 844 sheet: -0.49 (0.57), residues: 80 loop : -0.38 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 649 TYR 0.014 0.001 TYR B 138 PHE 0.015 0.001 PHE B 560 TRP 0.012 0.001 TRP B 397 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (12036) covalent geometry : angle 0.52781 / 0.28 (16326) SS BOND : bond 0.00287 / 0.15 ( 10) SS BOND : angle 1.51186 / 0.78 ( 20) hydrogen bonds : bond 0.03873 / 2.53 ( 688) hydrogen bonds : angle 4.24320 / 2.98 ( 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 210 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.8227 (t80) cc_final: 0.7967 (t80) REVERT: A 691 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8322 (tt) REVERT: A 711 PHE cc_start: 0.8579 (m-80) cc_final: 0.8335 (m-80) REVERT: A 786 ILE cc_start: 0.8894 (pt) cc_final: 0.8639 (mt) REVERT: B 659 MET cc_start: 0.8303 (mmm) cc_final: 0.7869 (mmm) REVERT: B 671 MET cc_start: 0.9037 (mmm) cc_final: 0.8755 (mmm) REVERT: B 691 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8312 (tt) REVERT: B 711 PHE cc_start: 0.8517 (m-80) cc_final: 0.8291 (m-80) REVERT: B 842 MET cc_start: 0.8746 (ttp) cc_final: 0.8410 (ttt) outliers start: 50 outliers final: 41 residues processed: 196 average time/residue: 0.0796 time to fit residues: 24.9145 Evaluate side-chains 195 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 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 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 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 248 LEU Chi-restraints excluded: chain B residue 249 HIS 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 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 652 GLN 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 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: 3.9990 chunk 25 optimal weight: 0.0770 chunk 61 optimal weight: 5.9990 chunk 136 optimal weight: 0.0010 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.7346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.186291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121256 restraints weight = 15956.877| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.77 r_work: 0.3356 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12046 Z= 0.109 Angle : 0.505 8.670 16346 Z= 0.263 Chirality : 0.038 0.150 1792 Planarity : 0.005 0.065 2016 Dihedral : 3.948 20.641 1566 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.41 % Allowed : 18.86 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.50 (0.23), residues: 1400 helix: 1.88 (0.18), residues: 848 sheet: -0.35 (0.58), residues: 80 loop : -0.33 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 649 TYR 0.012 0.001 TYR A 580 PHE 0.018 0.001 PHE B 183 TRP 0.013 0.001 TRP A 397 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (12036) covalent geometry : angle 0.50346 / 0.26 (16326) SS BOND : bond 0.00184 / 0.10 ( 10) SS BOND : angle 1.09890 / 0.59 ( 20) hydrogen bonds : bond 0.03536 / 2.31 ( 688) hydrogen bonds : angle 4.13244 / 2.89 ( 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 204 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.8232 (t80) cc_final: 0.8003 (t80) REVERT: A 652 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7874 (pp30) REVERT: A 711 PHE cc_start: 0.8505 (m-80) cc_final: 0.8256 (m-80) REVERT: A 786 ILE cc_start: 0.8896 (pt) cc_final: 0.8649 (mt) REVERT: B 671 MET cc_start: 0.8932 (mmm) cc_final: 0.8645 (mmm) REVERT: B 786 ILE cc_start: 0.8910 (pt) cc_final: 0.8673 (mt) REVERT: B 842 MET cc_start: 0.8681 (ttp) cc_final: 0.8381 (ttt) outliers start: 43 outliers final: 30 residues processed: 191 average time/residue: 0.0815 time to fit residues: 24.9262 Evaluate side-chains 179 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 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 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 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 717 GLU Chi-restraints excluded: chain A residue 807 CYS Chi-restraints excluded: chain B residue 62 LEU 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 601 CYS Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 807 CYS Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 65 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 115 optimal weight: 0.0070 chunk 61 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.7004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.185065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122169 restraints weight = 15906.536| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.64 r_work: 0.3293 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12046 Z= 0.146 Angle : 0.539 8.712 16346 Z= 0.279 Chirality : 0.039 0.151 1792 Planarity : 0.005 0.065 2016 Dihedral : 3.986 21.526 1566 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.65 % Allowed : 18.62 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.84 (0.18), residues: 848 sheet: -0.23 (0.59), residues: 80 loop : -0.36 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 649 TYR 0.011 0.001 TYR A 580 PHE 0.015 0.001 PHE A 560 TRP 0.010 0.001 TRP A 397 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12036) covalent geometry : angle 0.53777 / 0.28 (16326) SS BOND : bond 0.00203 / 0.12 ( 10) SS BOND : angle 1.19026 / 0.65 ( 20) hydrogen bonds : bond 0.03672 / 2.39 ( 688) hydrogen bonds : angle 4.13958 / 2.90 ( 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 202 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 PHE cc_start: 0.8277 (t80) cc_final: 0.8043 (t80) REVERT: A 671 MET cc_start: 0.9041 (mmm) cc_final: 0.8641 (mmm) REVERT: A 691 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8338 (tt) REVERT: A 711 PHE cc_start: 0.8578 (m-80) cc_final: 0.8329 (m-80) REVERT: A 786 ILE cc_start: 0.8947 (pt) cc_final: 0.8704 (mt) REVERT: A 842 MET cc_start: 0.8754 (ttp) cc_final: 0.8528 (ttt) REVERT: B 588 LEU cc_start: 0.8422 (pt) cc_final: 0.8203 (mm) REVERT: B 671 MET cc_start: 0.9043 (mmm) cc_final: 0.8778 (mmm) REVERT: B 691 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8337 (tt) REVERT: B 786 ILE cc_start: 0.8899 (pt) cc_final: 0.8674 (mt) REVERT: B 842 MET cc_start: 0.8716 (ttp) cc_final: 0.8426 (ttt) outliers start: 46 outliers final: 37 residues processed: 189 average time/residue: 0.0801 time to fit residues: 24.0464 Evaluate side-chains 190 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 248 LEU Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 339 ASP 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 606 THR 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 875 THR Chi-restraints excluded: chain B residue 62 LEU 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 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 652 GLN 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 875 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** 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 = 0.186114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120894 restraints weight = 15829.980| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.78 r_work: 0.3346 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12046 Z= 0.113 Angle : 0.523 9.043 16346 Z= 0.270 Chirality : 0.038 0.148 1792 Planarity : 0.005 0.064 2016 Dihedral : 3.921 20.776 1566 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.69 % Allowed : 19.65 % 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: 1.55 (0.23), residues: 1400 helix: 1.93 (0.18), residues: 848 sheet: 0.16 (0.62), residues: 70 loop : -0.44 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 649 TYR 0.012 0.001 TYR B 580 PHE 0.013 0.001 PHE B 253 TRP 0.013 0.001 TRP A 397 HIS 0.003 0.000 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (12036) covalent geometry : angle 0.52215 / 0.27 (16326) SS BOND : bond 0.00166 / 0.10 ( 10) SS BOND : angle 1.07648 / 0.59 ( 20) hydrogen bonds : bond 0.03508 / 2.29 ( 688) hydrogen bonds : angle 4.08817 / 2.86 ( 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 196 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8649 (pt0) cc_final: 0.8266 (pt0) REVERT: A 573 PHE cc_start: 0.8234 (t80) cc_final: 0.8005 (t80) REVERT: A 691 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8341 (tt) REVERT: A 711 PHE cc_start: 0.8556 (m-80) cc_final: 0.8343 (m-80) REVERT: A 786 ILE cc_start: 0.8944 (pt) cc_final: 0.8711 (mt) REVERT: B 588 LEU cc_start: 0.8373 (pt) cc_final: 0.8144 (mm) REVERT: B 671 MET cc_start: 0.8956 (mmm) cc_final: 0.8685 (mmm) REVERT: B 691 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8337 (tt) REVERT: B 842 MET cc_start: 0.8650 (ttp) cc_final: 0.8369 (ttt) outliers start: 34 outliers final: 31 residues processed: 185 average time/residue: 0.0762 time to fit residues: 22.4391 Evaluate side-chains 184 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 254 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 339 ASP 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 625 VAL 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 128 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 371 LEU 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 606 THR 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 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 875 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.185764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120177 restraints weight = 15790.208| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.79 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: 0.7905 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12046 Z= 0.124 Angle : 0.541 9.062 16346 Z= 0.279 Chirality : 0.038 0.149 1792 Planarity : 0.005 0.064 2016 Dihedral : 3.923 20.846 1566 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.01 % Allowed : 19.73 % Favored : 77.26 % 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: 1.54 (0.23), residues: 1400 helix: 1.91 (0.18), residues: 848 sheet: 0.19 (0.63), residues: 70 loop : -0.43 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.011 0.001 TYR B 580 PHE 0.021 0.001 PHE A 518 TRP 0.012 0.001 TRP B 359 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (12036) covalent geometry : angle 0.53980 / 0.28 (16326) SS BOND : bond 0.00184 / 0.11 ( 10) SS BOND : angle 1.12374 / 0.62 ( 20) hydrogen bonds : bond 0.03541 / 2.31 ( 688) hydrogen bonds : angle 4.07893 / 2.85 ( 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 198 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8669 (pt0) cc_final: 0.8281 (pt0) REVERT: A 573 PHE cc_start: 0.8238 (t80) cc_final: 0.8017 (t80) REVERT: A 691 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8346 (tt) REVERT: A 711 PHE cc_start: 0.8548 (m-80) cc_final: 0.8249 (m-80) REVERT: A 786 ILE cc_start: 0.8949 (pt) cc_final: 0.8718 (mt) REVERT: B 588 LEU cc_start: 0.8354 (pt) cc_final: 0.8127 (mm) REVERT: B 671 MET cc_start: 0.8983 (mmm) cc_final: 0.8722 (mmm) REVERT: B 691 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8335 (tt) REVERT: B 842 MET cc_start: 0.8615 (ttp) cc_final: 0.8358 (ttt) outliers start: 38 outliers final: 36 residues processed: 189 average time/residue: 0.0759 time to fit residues: 22.8018 Evaluate side-chains 190 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 254 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 339 ASP 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 606 THR 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 875 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 371 LEU 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 606 THR 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 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 875 THR 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: 2.9990 chunk 77 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4261 r_free = 0.4261 target = 0.187113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121795 restraints weight = 16002.085| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.81 r_work: 0.3361 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12046 Z= 0.110 Angle : 0.540 9.431 16346 Z= 0.278 Chirality : 0.038 0.148 1792 Planarity : 0.005 0.061 2016 Dihedral : 3.906 20.056 1566 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.01 % Allowed : 19.89 % Favored : 77.10 % 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: 1.58 (0.23), residues: 1400 helix: 1.95 (0.18), residues: 848 sheet: 0.23 (0.62), residues: 70 loop : -0.42 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.012 0.001 TYR B 580 PHE 0.018 0.001 PHE A 518 TRP 0.013 0.001 TRP B 397 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (12036) covalent geometry : angle 0.53884 / 0.28 (16326) SS BOND : bond 0.00155 / 0.09 ( 10) SS BOND : angle 1.06338 / 0.59 ( 20) hydrogen bonds : bond 0.03436 / 2.24 ( 688) hydrogen bonds : angle 4.06908 / 2.84 ( 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 200 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.8658 (pt0) cc_final: 0.8251 (pt0) REVERT: A 456 CYS cc_start: 0.7858 (m) cc_final: 0.7364 (p) REVERT: A 573 PHE cc_start: 0.8232 (t80) cc_final: 0.8007 (t80) REVERT: A 659 MET cc_start: 0.8341 (mmm) cc_final: 0.8091 (mmm) REVERT: A 691 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8326 (tt) REVERT: A 711 PHE cc_start: 0.8562 (m-80) cc_final: 0.8292 (m-80) REVERT: B 336 GLU cc_start: 0.8651 (pt0) cc_final: 0.8228 (pt0) REVERT: B 588 LEU cc_start: 0.8360 (pt) cc_final: 0.8129 (mm) REVERT: B 652 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7743 (pp30) REVERT: B 659 MET cc_start: 0.8357 (mmm) cc_final: 0.8137 (mmm) REVERT: B 691 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8332 (tt) REVERT: B 842 MET cc_start: 0.8593 (ttp) cc_final: 0.8322 (ttt) outliers start: 38 outliers final: 31 residues processed: 188 average time/residue: 0.0736 time to fit residues: 22.1758 Evaluate side-chains 184 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 401 GLN 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 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 875 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 371 LEU 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 606 THR Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 652 GLN 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 875 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 6 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 95 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4259 r_free = 0.4259 target = 0.186765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123697 restraints weight = 15912.628| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.20 r_work: 0.3344 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 12046 Z= 0.158 Angle : 0.792 59.199 16346 Z= 0.465 Chirality : 0.045 1.012 1792 Planarity : 0.005 0.064 2016 Dihedral : 3.900 20.077 1566 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.09 % Allowed : 19.81 % Favored : 77.10 % Cbeta Deviations : 0.07 % 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: 1.54 (0.23), residues: 1400 helix: 1.90 (0.18), residues: 848 sheet: 0.24 (0.62), residues: 70 loop : -0.43 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.011 0.001 TYR B 580 PHE 0.014 0.001 PHE A 518 TRP 0.012 0.001 TRP A 397 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (12036) covalent geometry : angle 0.79126 / 0.47 (16326) SS BOND : bond 0.00198 / 0.12 ( 10) SS BOND : angle 1.05378 / 0.59 ( 20) hydrogen bonds : bond 0.03536 / 2.33 ( 688) hydrogen bonds : angle 4.06968 / 2.84 ( 2022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.14 seconds wall clock time: 47 minutes 52.78 seconds (2872.78 seconds total)