Starting phenix.real_space_refine on Fri Jul 3 00:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iad_35300/07_2026/8iad_35300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iad_35300/07_2026/8iad_35300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8iad_35300/07_2026/8iad_35300.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iad_35300/07_2026/8iad_35300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iad_35300/07_2026/8iad_35300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iad_35300/07_2026/8iad_35300.map" model { file = "/net/cci-nas-00/data/ceres_data/8iad_35300/07_2026/8iad_35300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iad_35300/07_2026/8iad_35300.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 7198 2.51 5 N 1842 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11126 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5476 Classifications: {'peptide': 704} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 5476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5476 Classifications: {'peptide': 704} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 674} Chain breaks: 2 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 1, 'ATP': 1, 'NO3': 2, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 1, 'ATP': 1, 'NO3': 2, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.39, per 1000 atoms: 0.21 Number of scatterers: 11126 At special positions: 0 Unit cell: (80.704, 104, 106.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 12 15.00 Mg 2 11.99 O 2014 8.00 N 1842 7.00 C 7198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 405 " 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: 0.80 Conformation dependent library (CDL) restraints added in 483.9 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 6 sheets defined 61.8% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.512A pdb=" N ARG A 74 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 124 removed outlier: 4.119A pdb=" N TRP A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 154 removed outlier: 4.076A pdb=" N VAL A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 4.256A pdb=" N ALA A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 195 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.827A pdb=" N HIS A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 4.236A pdb=" N TYR A 234 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 236 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 258 removed outlier: 3.659A pdb=" N ARG A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 281 through 301 removed outlier: 3.565A pdb=" N PHE A 285 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 removed outlier: 3.520A pdb=" N LYS A 305 " --> pdb=" O ASN A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 331 through 363 removed outlier: 3.718A pdb=" N LYS A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 388 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.639A pdb=" N VAL A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.511A pdb=" N LEU A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 468 " --> pdb=" O CYS A 464 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 499 removed outlier: 3.954A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 490 " --> pdb=" O MET A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 523 Processing helix chain 'A' and resid 525 through 537 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 541 through 557 removed outlier: 3.582A pdb=" N MET A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 Processing helix chain 'A' and resid 588 through 594 Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.654A pdb=" N THR A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.620A pdb=" N LYS A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 671 removed outlier: 4.495A pdb=" N VAL A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 678 removed outlier: 3.569A pdb=" N GLU A 678 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.907A pdb=" N GLN A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 695 " --> pdb=" O GLU A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 695' Processing helix chain 'A' and resid 715 through 727 Processing helix chain 'A' and resid 750 through 755 removed outlier: 3.597A pdb=" N ARG A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 763 removed outlier: 3.655A pdb=" N GLN A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 762 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.512A pdb=" N ARG B 74 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 124 removed outlier: 4.119A pdb=" N TRP B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 154 removed outlier: 4.076A pdb=" N VAL B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 removed outlier: 4.144A pdb=" N ALA B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.828A pdb=" N HIS B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 4.235A pdb=" N TYR B 234 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN B 236 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 258 removed outlier: 3.660A pdb=" N ARG B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 281 through 301 removed outlier: 3.565A pdb=" N PHE B 285 " --> pdb=" O TRP B 281 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS B 301 " --> pdb=" O PHE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 removed outlier: 3.521A pdb=" N LYS B 305 " --> pdb=" O ASN B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 331 through 363 removed outlier: 3.719A pdb=" N LYS B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 388 Processing helix chain 'B' and resid 389 through 391 No H-bonds generated for 'chain 'B' and resid 389 through 391' Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.639A pdb=" N VAL B 439 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.511A pdb=" N LEU B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 468 " --> pdb=" O CYS B 464 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 499 removed outlier: 3.876A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 490 " --> pdb=" O MET B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 523 Processing helix chain 'B' and resid 525 through 537 Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 541 through 557 removed outlier: 3.583A pdb=" N MET B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 588 through 594 Processing helix chain 'B' and resid 607 through 618 removed outlier: 3.654A pdb=" N THR B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 652 removed outlier: 3.621A pdb=" N LYS B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 671 removed outlier: 4.495A pdb=" N VAL B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 removed outlier: 3.569A pdb=" N GLU B 678 " --> pdb=" O GLU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 695 removed outlier: 3.907A pdb=" N GLN B 694 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 695 " --> pdb=" O GLU B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 691 through 695' Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.596A pdb=" N ARG B 755 " --> pdb=" O ARG B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 763 removed outlier: 3.655A pdb=" N GLN B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 396 removed outlier: 3.568A pdb=" N LYS A 395 " --> pdb=" O TYR A 424 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.596A pdb=" N LEU A 602 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 639 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 711 removed outlier: 6.042A pdb=" N VAL A 710 " --> pdb=" O VAL A 734 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 395 through 396 removed outlier: 3.568A pdb=" N LYS B 395 " --> pdb=" O TYR B 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 602 through 603 removed outlier: 6.596A pdb=" N LEU B 602 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 639 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 709 through 711 removed outlier: 6.042A pdb=" N VAL B 710 " --> pdb=" O VAL B 734 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1680 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: 1.77 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2008 1.32 - 1.45: 2835 1.45 - 1.57: 6423 1.57 - 1.69: 18 1.69 - 1.81: 90 Bond restraints: 11374 Sorted by residual: bond pdb=" C4 ATP B 800 " pdb=" C5 ATP B 800 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C4 ATP A 800 " pdb=" C5 ATP A 800 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C5 ATP B 800 " pdb=" C6 ATP B 800 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.32e+01 bond pdb=" C5 ATP A 800 " pdb=" C6 ATP A 800 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.32e+01 bond pdb=" C5 ATP B 800 " pdb=" N7 ATP B 800 " ideal model delta sigma weight residual 1.387 1.334 0.053 1.00e-02 1.00e+04 2.80e+01 ... (remaining 11369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 15346 3.90 - 7.80: 115 7.80 - 11.70: 19 11.70 - 15.60: 0 15.60 - 19.50: 4 Bond angle restraints: 15484 Sorted by residual: angle pdb=" PB ATP B 800 " pdb=" O3B ATP B 800 " pdb=" PG ATP B 800 " ideal model delta sigma weight residual 139.87 120.37 19.50 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB ATP A 800 " pdb=" O3B ATP A 800 " pdb=" PG ATP A 800 " ideal model delta sigma weight residual 139.87 120.40 19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP B 800 " pdb=" O3A ATP B 800 " pdb=" PB ATP B 800 " ideal model delta sigma weight residual 136.83 120.48 16.35 1.00e+00 1.00e+00 2.67e+02 angle pdb=" PA ATP A 800 " pdb=" O3A ATP A 800 " pdb=" PB ATP A 800 " ideal model delta sigma weight residual 136.83 120.50 16.33 1.00e+00 1.00e+00 2.67e+02 angle pdb=" C5 ATP B 800 " pdb=" C4 ATP B 800 " pdb=" N3 ATP B 800 " ideal model delta sigma weight residual 126.80 117.52 9.28 1.00e+00 1.00e+00 8.61e+01 ... (remaining 15479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 5761 16.11 - 32.22: 703 32.22 - 48.33: 118 48.33 - 64.44: 20 64.44 - 80.55: 12 Dihedral angle restraints: 6614 sinusoidal: 2594 harmonic: 4020 Sorted by residual: dihedral pdb=" CB CYS A 397 " pdb=" SG CYS A 397 " pdb=" SG CYS A 405 " pdb=" CB CYS A 405 " ideal model delta sinusoidal sigma weight residual 93.00 170.30 -77.30 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS B 397 " pdb=" SG CYS B 397 " pdb=" SG CYS B 405 " pdb=" CB CYS B 405 " ideal model delta sinusoidal sigma weight residual 93.00 170.29 -77.29 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CA THR B 554 " pdb=" C THR B 554 " pdb=" N VAL B 555 " pdb=" CA VAL B 555 " ideal model delta harmonic sigma weight residual 180.00 155.78 24.22 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 6611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1462 0.070 - 0.141: 299 0.141 - 0.211: 44 0.211 - 0.282: 3 0.282 - 0.352: 2 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CB VAL B 319 " pdb=" CA VAL B 319 " pdb=" CG1 VAL B 319 " pdb=" CG2 VAL B 319 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB VAL A 319 " pdb=" CA VAL A 319 " pdb=" CG1 VAL A 319 " pdb=" CG2 VAL A 319 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C2C PIO A 804 " pdb=" C1C PIO A 804 " pdb=" C3C PIO A 804 " pdb=" O2C PIO A 804 " both_signs ideal model delta sigma weight residual False -2.56 -2.30 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1807 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 402 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" CG ASP B 402 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASP B 402 " 0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP B 402 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 402 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" CG ASP A 402 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASP A 402 " -0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP A 402 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 402 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C ASP B 402 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP B 402 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU B 403 " -0.018 2.00e-02 2.50e+03 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 82 2.55 - 3.14: 8366 3.14 - 3.72: 17066 3.72 - 4.31: 24249 4.31 - 4.90: 41234 Nonbonded interactions: 90997 Sorted by model distance: nonbonded pdb=" O1B ATP A 800 " pdb="MG MG A 801 " model vdw 1.961 2.170 nonbonded pdb=" O1B ATP B 800 " pdb="MG MG B 801 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU B 55 " pdb="MG MG B 801 " model vdw 2.123 2.170 nonbonded pdb=" OE1 GLU A 55 " pdb="MG MG A 801 " model vdw 2.171 2.170 nonbonded pdb=" O VAL B 614 " pdb=" OG1 THR B 618 " model vdw 2.274 3.040 ... (remaining 90992 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: 0.01 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: 2.410 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.010 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 11380 Z= 0.432 Angle : 1.026 19.505 15496 Z= 0.619 Chirality : 0.058 0.352 1810 Planarity : 0.007 0.058 1918 Dihedral : 14.227 80.551 4020 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 0.25 % Allowed : 10.32 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -4.34 (0.16), residues: 1396 helix: -2.86 (0.12), residues: 832 sheet: None (None), residues: 0 loop : -2.71 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 325 TYR 0.013 0.002 TYR A 463 PHE 0.027 0.003 PHE B 417 TRP 0.011 0.002 TRP A 274 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00945 / 0.43 (11374) covalent geometry : angle 1.02632 / 0.62 (15484) SS BOND : bond 0.00171 / 0.09 ( 6) SS BOND : angle 0.81653 / 0.43 ( 12) hydrogen bonds : bond 0.12693 / 7.80 ( 570) hydrogen bonds : angle 5.84691 / 4.19 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.328 Fit side-chains REVERT: A 184 MET cc_start: 0.7628 (mmt) cc_final: 0.7315 (mmm) REVERT: A 200 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8323 (pp) REVERT: A 658 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7346 (mm-30) REVERT: B 184 MET cc_start: 0.7613 (mmt) cc_final: 0.7301 (mmm) REVERT: B 200 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8315 (pp) REVERT: B 658 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7424 (mm-30) outliers start: 3 outliers final: 0 residues processed: 164 average time/residue: 0.1106 time to fit residues: 24.5659 Evaluate side-chains 116 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN A 327 HIS A 503 ASN A 569 HIS A 586 ASN A 593 ASN A 730 HIS A 758 ASN A 761 GLN B 125 GLN B 327 HIS B 503 ASN B 569 HIS B 586 ASN B 593 ASN B 730 HIS B 758 ASN B 761 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101460 restraints weight = 12509.345| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.54 r_work: 0.3002 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11380 Z= 0.127 Angle : 0.558 7.058 15496 Z= 0.291 Chirality : 0.040 0.125 1810 Planarity : 0.004 0.042 1918 Dihedral : 6.725 58.286 1550 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.51 % Allowed : 14.51 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.14 (0.20), residues: 1396 helix: -0.88 (0.17), residues: 826 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 661 TYR 0.013 0.001 TYR A 121 PHE 0.022 0.001 PHE A 723 TRP 0.008 0.001 TRP A 129 HIS 0.010 0.001 HIS B 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (11374) covalent geometry : angle 0.55839 / 0.29 (15484) SS BOND : bond 0.00135 / 0.07 ( 6) SS BOND : angle 0.45029 / 0.23 ( 12) hydrogen bonds : bond 0.03815 / 2.46 ( 570) hydrogen bonds : angle 4.31824 / 3.05 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.288 Fit side-chains REVERT: A 121 TYR cc_start: 0.7950 (t80) cc_final: 0.7682 (t80) REVERT: A 164 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6130 (mt-10) REVERT: A 177 MET cc_start: 0.8720 (tpp) cc_final: 0.8494 (tpp) REVERT: A 203 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: A 550 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6304 (mm) REVERT: A 658 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 121 TYR cc_start: 0.7971 (t80) cc_final: 0.7698 (t80) REVERT: B 164 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6263 (mt-10) REVERT: B 177 MET cc_start: 0.8676 (tpp) cc_final: 0.8453 (tpp) REVERT: B 203 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: B 550 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6364 (mm) outliers start: 18 outliers final: 6 residues processed: 144 average time/residue: 0.0945 time to fit residues: 19.3103 Evaluate side-chains 128 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 503 ASN A 569 HIS A 620 HIS A 752 GLN B 327 HIS B 503 ASN B 569 HIS B 620 HIS B 752 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099960 restraints weight = 12752.359| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.56 r_work: 0.2977 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11380 Z= 0.155 Angle : 0.554 7.448 15496 Z= 0.284 Chirality : 0.041 0.124 1810 Planarity : 0.004 0.038 1918 Dihedral : 6.373 55.462 1546 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.68 % Allowed : 15.94 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.36 (0.21), residues: 1396 helix: -0.23 (0.18), residues: 820 sheet: None (None), residues: 0 loop : -1.84 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 258 TYR 0.010 0.001 TYR A 121 PHE 0.018 0.001 PHE A 723 TRP 0.007 0.001 TRP A 129 HIS 0.011 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (11374) covalent geometry : angle 0.55397 / 0.28 (15484) SS BOND : bond 0.00193 / 0.11 ( 6) SS BOND : angle 0.45203 / 0.23 ( 12) hydrogen bonds : bond 0.03739 / 2.41 ( 570) hydrogen bonds : angle 4.12222 / 2.91 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.289 Fit side-chains REVERT: A 121 TYR cc_start: 0.7918 (t80) cc_final: 0.7675 (t80) REVERT: A 164 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6128 (mt-10) REVERT: A 658 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 753 ASP cc_start: 0.8546 (m-30) cc_final: 0.8144 (m-30) REVERT: B 121 TYR cc_start: 0.7917 (t80) cc_final: 0.7666 (t80) REVERT: B 164 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6196 (mt-10) REVERT: B 284 PHE cc_start: 0.6004 (t80) cc_final: 0.5721 (t80) REVERT: B 550 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6352 (mm) REVERT: B 658 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7560 (mm-30) REVERT: B 753 ASP cc_start: 0.8553 (m-30) cc_final: 0.8116 (m-30) outliers start: 32 outliers final: 20 residues processed: 146 average time/residue: 0.0852 time to fit residues: 18.0356 Evaluate side-chains 138 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 HIS A 752 GLN B 569 HIS B 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100930 restraints weight = 12768.586| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.59 r_work: 0.2978 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11380 Z= 0.157 Angle : 0.545 7.663 15496 Z= 0.278 Chirality : 0.041 0.124 1810 Planarity : 0.004 0.039 1918 Dihedral : 6.220 55.508 1546 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.19 % Allowed : 16.28 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.97 (0.22), residues: 1396 helix: 0.06 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 258 TYR 0.009 0.001 TYR B 463 PHE 0.018 0.001 PHE A 723 TRP 0.007 0.001 TRP B 129 HIS 0.011 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (11374) covalent geometry : angle 0.54485 / 0.28 (15484) SS BOND : bond 0.00182 / 0.11 ( 6) SS BOND : angle 0.43223 / 0.23 ( 12) hydrogen bonds : bond 0.03636 / 2.34 ( 570) hydrogen bonds : angle 4.04521 / 2.85 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.262 Fit side-chains REVERT: A 121 TYR cc_start: 0.7894 (t80) cc_final: 0.7674 (t80) REVERT: A 164 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6393 (mt-10) REVERT: A 203 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7362 (mm-30) REVERT: A 658 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 753 ASP cc_start: 0.8547 (m-30) cc_final: 0.8103 (m-30) REVERT: B 121 TYR cc_start: 0.7891 (t80) cc_final: 0.7652 (t80) REVERT: B 164 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6356 (mt-10) REVERT: B 203 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: B 753 ASP cc_start: 0.8547 (m-30) cc_final: 0.8082 (m-30) outliers start: 38 outliers final: 27 residues processed: 144 average time/residue: 0.0820 time to fit residues: 17.8197 Evaluate side-chains 150 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 ASN A 569 HIS ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN B 408 ASN B 569 HIS ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096965 restraints weight = 12984.640| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.58 r_work: 0.2914 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11380 Z= 0.253 Angle : 0.632 9.264 15496 Z= 0.319 Chirality : 0.045 0.139 1810 Planarity : 0.004 0.039 1918 Dihedral : 6.571 57.980 1546 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.10 % Allowed : 18.62 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.22), residues: 1396 helix: -0.09 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -1.57 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 653 TYR 0.009 0.001 TYR A 424 PHE 0.019 0.002 PHE B 723 TRP 0.009 0.001 TRP A 274 HIS 0.010 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.25 (11374) covalent geometry : angle 0.63219 / 0.32 (15484) SS BOND : bond 0.00260 / 0.15 ( 6) SS BOND : angle 0.52405 / 0.28 ( 12) hydrogen bonds : bond 0.04160 / 2.66 ( 570) hydrogen bonds : angle 4.17983 / 2.95 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.280 Fit side-chains REVERT: A 121 TYR cc_start: 0.7894 (t80) cc_final: 0.7694 (t80) REVERT: A 164 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6304 (mt-10) REVERT: A 177 MET cc_start: 0.8634 (tpp) cc_final: 0.8366 (tpp) REVERT: A 284 PHE cc_start: 0.6158 (t80) cc_final: 0.5915 (t80) REVERT: A 427 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6454 (tt) REVERT: A 550 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6430 (mm) REVERT: A 658 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 121 TYR cc_start: 0.7899 (t80) cc_final: 0.7693 (t80) REVERT: B 164 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6264 (mt-10) REVERT: B 177 MET cc_start: 0.8601 (tpp) cc_final: 0.8094 (tpt) REVERT: B 427 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6472 (tt) REVERT: B 658 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7647 (mm-30) outliers start: 37 outliers final: 29 residues processed: 139 average time/residue: 0.0786 time to fit residues: 16.3753 Evaluate side-chains 143 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 ASN A 569 HIS A 752 GLN B 569 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.101793 restraints weight = 12786.420| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.58 r_work: 0.2991 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11380 Z= 0.123 Angle : 0.520 7.440 15496 Z= 0.266 Chirality : 0.040 0.125 1810 Planarity : 0.003 0.040 1918 Dihedral : 6.113 57.998 1546 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.02 % Allowed : 18.29 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.53 (0.22), residues: 1396 helix: 0.31 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.017 0.001 TYR A 463 PHE 0.018 0.001 PHE A 723 TRP 0.006 0.001 TRP B 129 HIS 0.010 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (11374) covalent geometry : angle 0.52031 / 0.27 (15484) SS BOND : bond 0.00164 / 0.10 ( 6) SS BOND : angle 0.39204 / 0.20 ( 12) hydrogen bonds : bond 0.03440 / 2.23 ( 570) hydrogen bonds : angle 3.98516 / 2.80 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: A 550 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6347 (mm) REVERT: A 658 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 753 ASP cc_start: 0.8425 (m-30) cc_final: 0.8066 (m-30) REVERT: B 177 MET cc_start: 0.8566 (tpp) cc_final: 0.8194 (tpt) REVERT: B 203 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: B 658 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7597 (mm-30) REVERT: B 753 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8142 (m-30) outliers start: 36 outliers final: 23 residues processed: 138 average time/residue: 0.0830 time to fit residues: 16.9379 Evaluate side-chains 141 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 753 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 503 ASN A 569 HIS A 752 GLN B 569 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102000 restraints weight = 12617.915| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.56 r_work: 0.2997 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11380 Z= 0.126 Angle : 0.518 7.160 15496 Z= 0.264 Chirality : 0.040 0.123 1810 Planarity : 0.003 0.040 1918 Dihedral : 5.951 59.236 1546 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.44 % Allowed : 18.46 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.25 (0.22), residues: 1396 helix: 0.53 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -1.14 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.014 0.001 TYR B 463 PHE 0.017 0.001 PHE A 723 TRP 0.006 0.001 TRP A 457 HIS 0.011 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11374) covalent geometry : angle 0.51846 / 0.26 (15484) SS BOND : bond 0.00164 / 0.09 ( 6) SS BOND : angle 0.43312 / 0.23 ( 12) hydrogen bonds : bond 0.03396 / 2.19 ( 570) hydrogen bonds : angle 3.91560 / 2.75 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6322 (mt-10) REVERT: A 203 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: A 403 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: A 493 MET cc_start: 0.7049 (mtp) cc_final: 0.6730 (mtp) REVERT: A 658 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7646 (mm-30) REVERT: A 753 ASP cc_start: 0.8434 (m-30) cc_final: 0.8070 (m-30) REVERT: B 177 MET cc_start: 0.8516 (tpp) cc_final: 0.8183 (tpt) REVERT: B 203 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: B 403 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: B 493 MET cc_start: 0.7080 (mtp) cc_final: 0.6767 (mtp) REVERT: B 550 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6281 (mm) REVERT: B 658 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 753 ASP cc_start: 0.8491 (m-30) cc_final: 0.8101 (m-30) outliers start: 41 outliers final: 27 residues processed: 137 average time/residue: 0.0808 time to fit residues: 16.6634 Evaluate side-chains 143 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 0.0770 chunk 110 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 ASN A 569 HIS B 569 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101588 restraints weight = 12594.359| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.56 r_work: 0.2991 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11380 Z= 0.136 Angle : 0.521 7.001 15496 Z= 0.265 Chirality : 0.040 0.123 1810 Planarity : 0.003 0.040 1918 Dihedral : 5.886 56.340 1546 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.61 % Allowed : 18.62 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.14 (0.22), residues: 1396 helix: 0.60 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 653 TYR 0.013 0.001 TYR B 463 PHE 0.017 0.001 PHE B 723 TRP 0.006 0.001 TRP B 129 HIS 0.011 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (11374) covalent geometry : angle 0.52123 / 0.26 (15484) SS BOND : bond 0.00153 / 0.09 ( 6) SS BOND : angle 0.42007 / 0.22 ( 12) hydrogen bonds : bond 0.03433 / 2.21 ( 570) hydrogen bonds : angle 3.90581 / 2.74 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6417 (mt-10) REVERT: A 203 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: A 403 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: A 427 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6585 (tt) REVERT: A 493 MET cc_start: 0.7118 (mtp) cc_final: 0.6774 (mtp) REVERT: A 658 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7649 (mm-30) REVERT: A 753 ASP cc_start: 0.8476 (m-30) cc_final: 0.8124 (m-30) REVERT: B 177 MET cc_start: 0.8492 (tpp) cc_final: 0.8171 (tpt) REVERT: B 203 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7361 (mm-30) REVERT: B 403 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: B 493 MET cc_start: 0.7115 (mtp) cc_final: 0.6769 (mtp) REVERT: B 550 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6281 (mm) REVERT: B 658 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7529 (mm-30) REVERT: B 753 ASP cc_start: 0.8513 (m-30) cc_final: 0.8112 (m-30) outliers start: 43 outliers final: 28 residues processed: 136 average time/residue: 0.0842 time to fit residues: 17.3883 Evaluate side-chains 145 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 103 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 503 ASN A 569 HIS B 569 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104572 restraints weight = 12532.886| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.56 r_work: 0.3023 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11380 Z= 0.103 Angle : 0.489 5.932 15496 Z= 0.249 Chirality : 0.039 0.125 1810 Planarity : 0.003 0.041 1918 Dihedral : 5.618 56.016 1546 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.10 % Allowed : 19.30 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.15 (0.23), residues: 1396 helix: 0.81 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.91 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.012 0.001 TYR A 463 PHE 0.016 0.001 PHE B 723 TRP 0.008 0.001 TRP A 457 HIS 0.011 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (11374) covalent geometry : angle 0.48950 / 0.25 (15484) SS BOND : bond 0.00131 / 0.07 ( 6) SS BOND : angle 0.39417 / 0.20 ( 12) hydrogen bonds : bond 0.03170 / 2.06 ( 570) hydrogen bonds : angle 3.81591 / 2.68 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.267 Fit side-chains REVERT: A 164 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6424 (mt-10) REVERT: A 203 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: A 403 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: A 493 MET cc_start: 0.7018 (mtp) cc_final: 0.6681 (mtp) REVERT: A 658 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 753 ASP cc_start: 0.8471 (m-30) cc_final: 0.8161 (m-30) REVERT: B 164 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6496 (mt-10) REVERT: B 203 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: B 403 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: B 427 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6644 (tt) REVERT: B 493 MET cc_start: 0.7077 (mtp) cc_final: 0.6703 (mtp) REVERT: B 753 ASP cc_start: 0.8495 (m-30) cc_final: 0.8139 (m-30) outliers start: 37 outliers final: 25 residues processed: 144 average time/residue: 0.0746 time to fit residues: 16.5218 Evaluate side-chains 146 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 ASN A 569 HIS B 569 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102923 restraints weight = 12689.060| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.57 r_work: 0.3002 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11380 Z= 0.127 Angle : 0.512 6.815 15496 Z= 0.259 Chirality : 0.040 0.121 1810 Planarity : 0.003 0.040 1918 Dihedral : 5.699 55.345 1546 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.94 % Allowed : 19.21 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.21 (0.23), residues: 1396 helix: 0.87 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.012 0.001 TYR B 463 PHE 0.016 0.001 PHE B 723 TRP 0.006 0.001 TRP B 457 HIS 0.011 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11374) covalent geometry : angle 0.51165 / 0.26 (15484) SS BOND : bond 0.00141 / 0.08 ( 6) SS BOND : angle 0.42736 / 0.22 ( 12) hydrogen bonds : bond 0.03321 / 2.14 ( 570) hydrogen bonds : angle 3.82367 / 2.69 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.257 Fit side-chains REVERT: A 164 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6550 (mt-10) REVERT: A 203 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: A 403 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: A 493 MET cc_start: 0.7138 (mtp) cc_final: 0.6782 (mtp) REVERT: A 658 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 753 ASP cc_start: 0.8489 (m-30) cc_final: 0.8172 (m-30) REVERT: B 164 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6430 (mt-10) REVERT: B 177 MET cc_start: 0.8765 (tpp) cc_final: 0.8490 (tpp) REVERT: B 203 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: B 403 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: B 427 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6730 (tt) REVERT: B 493 MET cc_start: 0.7149 (mtp) cc_final: 0.6794 (mtp) REVERT: B 658 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 753 ASP cc_start: 0.8517 (m-30) cc_final: 0.8146 (m-30) outliers start: 35 outliers final: 27 residues processed: 132 average time/residue: 0.0754 time to fit residues: 15.0562 Evaluate side-chains 142 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 0.0970 chunk 71 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS A 503 ASN A 569 HIS B 569 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102540 restraints weight = 12684.672| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.57 r_work: 0.3002 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11380 Z= 0.131 Angle : 0.514 6.489 15496 Z= 0.260 Chirality : 0.040 0.121 1810 Planarity : 0.003 0.040 1918 Dihedral : 5.663 56.864 1546 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.10 % Allowed : 19.13 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.28 (0.23), residues: 1396 helix: 0.92 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -0.83 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.012 0.001 TYR B 463 PHE 0.017 0.001 PHE B 723 TRP 0.006 0.001 TRP B 129 HIS 0.011 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (11374) covalent geometry : angle 0.51400 / 0.26 (15484) SS BOND : bond 0.00142 / 0.08 ( 6) SS BOND : angle 0.44454 / 0.23 ( 12) hydrogen bonds : bond 0.03347 / 2.16 ( 570) hydrogen bonds : angle 3.82264 / 2.68 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.58 seconds wall clock time: 30 minutes 48.84 seconds (1848.84 seconds total)