Starting phenix.real_space_refine on Fri Sep 11 14:50:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p48_20246/09_2026/6p48_20246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p48_20246/09_2026/6p48_20246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p48_20246/09_2026/6p48_20246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p48_20246/09_2026/6p48_20246.map" model { file = "/net/cci-nas-00/data/ceres_data/6p48_20246/09_2026/6p48_20246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p48_20246/09_2026/6p48_20246.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6p48_20246/09_2026/6p48_20246.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p48_20246/09_2026/6p48_20246.cif" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 68 5.16 5 C 6592 2.51 5 N 1586 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9936 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4967 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 577} Chain breaks: 9 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 4.27, per 1000 atoms: 0.43 Number of scatterers: 9936 At special positions: 0 Unit cell: (85.779, 112.254, 109.077, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 68 16.00 O 1688 8.00 N 1586 7.00 C 6592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 293.9 milliseconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 60.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 91 through 104 removed outlier: 3.994A pdb=" N LYS A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.787A pdb=" N ARG A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.626A pdb=" N VAL A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.685A pdb=" N TRP A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 326 removed outlier: 3.834A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.837A pdb=" N SER A 376 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 408 removed outlier: 3.856A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.558A pdb=" N CYS A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 456' Processing helix chain 'A' and resid 456 through 480 removed outlier: 3.729A pdb=" N PHE A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.648A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 537 removed outlier: 3.818A pdb=" N PHE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.906A pdb=" N TYR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 573 removed outlier: 4.589A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 572 " --> pdb=" O PHE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.583A pdb=" N LEU A 588 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 614 removed outlier: 3.535A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 638 through 646 removed outlier: 3.555A pdb=" N GLY A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 removed outlier: 3.543A pdb=" N ASP A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 removed outlier: 3.765A pdb=" N GLU A 670 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.597A pdb=" N ASN A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.518A pdb=" N ALA A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.603A pdb=" N TYR A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.511A pdb=" N SER A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 104 removed outlier: 3.995A pdb=" N LYS B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.787A pdb=" N ARG B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 239 removed outlier: 3.626A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.685A pdb=" N TRP B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 326 removed outlier: 3.834A pdb=" N VAL B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.837A pdb=" N SER B 376 " --> pdb=" O CYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 408 removed outlier: 3.856A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.557A pdb=" N CYS B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 456' Processing helix chain 'B' and resid 456 through 480 removed outlier: 3.728A pdb=" N PHE B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.648A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 537 removed outlier: 3.818A pdb=" N PHE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 535 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.906A pdb=" N TYR B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASN B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 573 removed outlier: 4.590A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.583A pdb=" N LEU B 588 " --> pdb=" O VAL B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.535A pdb=" N LEU B 605 " --> pdb=" O CYS B 601 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 638 through 646 removed outlier: 3.555A pdb=" N GLY B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 654 removed outlier: 3.542A pdb=" N ASP B 653 " --> pdb=" O ARG B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 3.765A pdb=" N GLU B 670 " --> pdb=" O TYR B 666 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.597A pdb=" N ASN B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 3.518A pdb=" N ALA B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.602A pdb=" N TYR B 756 " --> pdb=" O PRO B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.510A pdb=" N SER B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 removed outlier: 3.534A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.534A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1248 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: 1.21 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2934 1.34 - 1.47: 2832 1.47 - 1.59: 4334 1.59 - 1.72: 0 1.72 - 1.84: 106 Bond restraints: 10206 Sorted by residual: bond pdb=" CA ALA A 571 " pdb=" C ALA A 571 " ideal model delta sigma weight residual 1.524 1.577 -0.054 1.16e-02 7.43e+03 2.15e+01 bond pdb=" CA ALA B 571 " pdb=" C ALA B 571 " ideal model delta sigma weight residual 1.524 1.577 -0.053 1.16e-02 7.43e+03 2.12e+01 bond pdb=" CA PHE A 812 " pdb=" CB PHE A 812 " ideal model delta sigma weight residual 1.526 1.464 0.063 1.53e-02 4.27e+03 1.68e+01 bond pdb=" CA PHE B 812 " pdb=" CB PHE B 812 " ideal model delta sigma weight residual 1.526 1.464 0.063 1.53e-02 4.27e+03 1.68e+01 bond pdb=" N PRO B 648 " pdb=" CD PRO B 648 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 ... (remaining 10201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 13089 3.04 - 6.08: 614 6.08 - 9.12: 103 9.12 - 12.16: 26 12.16 - 15.19: 12 Bond angle restraints: 13844 Sorted by residual: angle pdb=" N ARG A 478 " pdb=" CA ARG A 478 " pdb=" C ARG A 478 " ideal model delta sigma weight residual 113.88 100.31 13.57 1.23e+00 6.61e-01 1.22e+02 angle pdb=" N ARG B 478 " pdb=" CA ARG B 478 " pdb=" C ARG B 478 " ideal model delta sigma weight residual 113.88 100.33 13.55 1.23e+00 6.61e-01 1.21e+02 angle pdb=" N ALA A 274 " pdb=" CA ALA A 274 " pdb=" C ALA A 274 " ideal model delta sigma weight residual 112.68 126.47 -13.79 1.33e+00 5.65e-01 1.07e+02 angle pdb=" N ALA B 274 " pdb=" CA ALA B 274 " pdb=" C ALA B 274 " ideal model delta sigma weight residual 112.68 126.44 -13.76 1.33e+00 5.65e-01 1.07e+02 angle pdb=" N LEU B 664 " pdb=" CA LEU B 664 " pdb=" C LEU B 664 " ideal model delta sigma weight residual 112.59 100.75 11.84 1.22e+00 6.72e-01 9.42e+01 ... (remaining 13839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 5026 16.48 - 32.95: 728 32.95 - 49.43: 164 49.43 - 65.90: 50 65.90 - 82.38: 8 Dihedral angle restraints: 5976 sinusoidal: 2410 harmonic: 3566 Sorted by residual: dihedral pdb=" CA ILE A 786 " pdb=" C ILE A 786 " pdb=" N THR A 787 " pdb=" CA THR A 787 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE B 786 " pdb=" C ILE B 786 " pdb=" N THR B 787 " pdb=" CA THR B 787 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP A 375 " pdb=" C ASP A 375 " pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 5973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1318 0.105 - 0.210: 162 0.210 - 0.315: 30 0.315 - 0.421: 24 0.421 - 0.526: 4 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA ALA B 274 " pdb=" N ALA B 274 " pdb=" C ALA B 274 " pdb=" CB ALA B 274 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CA ALA A 274 " pdb=" N ALA A 274 " pdb=" C ALA A 274 " pdb=" CB ALA A 274 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CA PRO A 340 " pdb=" N PRO A 340 " pdb=" C PRO A 340 " pdb=" CB PRO A 340 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 1535 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 541 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" C PRO A 541 " -0.074 2.00e-02 2.50e+03 pdb=" O PRO A 541 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG A 542 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 541 " 0.021 2.00e-02 2.50e+03 4.27e-02 1.82e+01 pdb=" C PRO B 541 " -0.074 2.00e-02 2.50e+03 pdb=" O PRO B 541 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG B 542 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 647 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 648 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.055 5.00e-02 4.00e+02 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 156 2.59 - 3.17: 8430 3.17 - 3.75: 16032 3.75 - 4.32: 22064 4.32 - 4.90: 34337 Nonbonded interactions: 81019 Sorted by model distance: nonbonded pdb=" CD1 LEU A 627 " pdb=" CD PRO A 628 " model vdw 2.014 3.860 nonbonded pdb=" CD1 LEU B 627 " pdb=" CD PRO B 628 " model vdw 2.014 3.860 nonbonded pdb=" CB HIS B 275 " pdb=" CD PRO B 276 " model vdw 2.171 3.840 nonbonded pdb=" CB HIS A 275 " pdb=" CD PRO A 276 " model vdw 2.171 3.840 nonbonded pdb=" O HIS B 275 " pdb=" O SER B 278 " model vdw 2.200 3.040 ... (remaining 81014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 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 : 0.011 0.100 10214 Z= 0.493 Angle : 1.557 15.195 13860 Z= 0.962 Chirality : 0.091 0.526 1538 Planarity : 0.011 0.103 1686 Dihedral : 16.573 82.380 3656 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.51 % Favored : 92.64 % Rotamer: Outliers : 3.53 % Allowed : 14.68 % Favored : 81.78 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.05 (0.17), residues: 1168 helix: -4.12 (0.11), residues: 696 sheet: -3.70 (1.03), residues: 18 loop : -3.59 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 209 TYR 0.037 0.004 TYR A 809 PHE 0.028 0.004 PHE B 760 TRP 0.039 0.004 TRP B 463 HIS 0.008 0.002 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.01065 / 0.49 (10206) covalent geometry : angle 1.55569 / 0.96 (13844) SS BOND : bond 0.00385 / 0.16 ( 8) SS BOND : angle 2.24811 / 1.35 ( 16) hydrogen bonds : bond 0.30919 / 19.55 ( 418) hydrogen bonds : angle 12.12342 / 8.37 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.5230 (OUTLIER) cc_final: 0.4889 (t70) REVERT: A 298 ILE cc_start: 0.8456 (tp) cc_final: 0.8144 (tt) REVERT: A 396 PHE cc_start: 0.6698 (t80) cc_final: 0.6483 (t80) REVERT: A 403 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 588 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5903 (mm) REVERT: A 590 LYS cc_start: 0.4367 (OUTLIER) cc_final: 0.3613 (mppt) REVERT: A 671 MET cc_start: 0.8217 (mmm) cc_final: 0.7676 (mmm) REVERT: A 742 MET cc_start: 0.7116 (mmt) cc_final: 0.6810 (tpp) REVERT: A 826 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4984 (pt) REVERT: A 853 ILE cc_start: 0.8491 (mm) cc_final: 0.8249 (mt) REVERT: B 275 HIS cc_start: 0.5514 (OUTLIER) cc_final: 0.4570 (t70) REVERT: B 298 ILE cc_start: 0.8361 (tp) cc_final: 0.8095 (tt) REVERT: B 403 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 590 LYS cc_start: 0.4209 (OUTLIER) cc_final: 0.3396 (mmtt) REVERT: B 649 ARG cc_start: 0.6494 (pmt170) cc_final: 0.6141 (ptt-90) REVERT: B 750 MET cc_start: 0.5962 (mmp) cc_final: 0.5059 (ttm) outliers start: 38 outliers final: 9 residues processed: 233 average time/residue: 0.1009 time to fit residues: 32.7627 Evaluate side-chains 153 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 862 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 129 HIS A 275 HIS A 283 GLN A 620 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN A 726 GLN A 740 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN B 99 GLN B 129 HIS B 275 HIS B 620 ASN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN B 726 GLN B 740 ASN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.232274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.201391 restraints weight = 14811.332| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 3.45 r_work: 0.4261 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10214 Z= 0.186 Angle : 0.816 14.661 13860 Z= 0.433 Chirality : 0.047 0.187 1538 Planarity : 0.007 0.059 1686 Dihedral : 8.623 59.009 1361 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.76 % Favored : 93.07 % Rotamer: Outliers : 4.37 % Allowed : 15.89 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -4.55 (0.20), residues: 1168 helix: -2.80 (0.15), residues: 712 sheet: -3.50 (0.76), residues: 26 loop : -3.12 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 542 TYR 0.034 0.002 TYR A 323 PHE 0.021 0.002 PHE A 851 TRP 0.028 0.003 TRP B 629 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (10206) covalent geometry : angle 0.81502 / 0.43 (13844) SS BOND : bond 0.00270 / 0.12 ( 8) SS BOND : angle 1.44343 / 0.71 ( 16) hydrogen bonds : bond 0.06690 / 4.37 ( 418) hydrogen bonds : angle 7.22859 / 5.02 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6029 (OUTLIER) cc_final: 0.4759 (t-90) REVERT: A 298 ILE cc_start: 0.8149 (tp) cc_final: 0.7810 (tt) REVERT: A 403 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 522 MET cc_start: 0.7190 (mmp) cc_final: 0.6906 (mmm) REVERT: A 588 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5770 (mm) REVERT: A 742 MET cc_start: 0.7805 (mmt) cc_final: 0.7567 (tpp) REVERT: A 857 ILE cc_start: 0.7524 (tp) cc_final: 0.7253 (tt) REVERT: B 101 TYR cc_start: 0.6237 (t80) cc_final: 0.6026 (t80) REVERT: B 270 TYR cc_start: 0.5306 (t80) cc_final: 0.4895 (t80) REVERT: B 275 HIS cc_start: 0.6596 (OUTLIER) cc_final: 0.5105 (t-90) REVERT: B 298 ILE cc_start: 0.8165 (tp) cc_final: 0.7862 (tt) REVERT: B 323 TYR cc_start: 0.7803 (p90) cc_final: 0.7586 (p90) REVERT: B 403 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7586 (tm-30) REVERT: B 461 PHE cc_start: 0.8339 (m-10) cc_final: 0.8092 (m-80) REVERT: B 590 LYS cc_start: 0.4815 (OUTLIER) cc_final: 0.3754 (mmtt) REVERT: B 629 TRP cc_start: 0.5532 (m-90) cc_final: 0.4898 (m100) REVERT: B 649 ARG cc_start: 0.6835 (pmt170) cc_final: 0.6519 (ptt-90) REVERT: B 857 ILE cc_start: 0.7473 (tp) cc_final: 0.7227 (tt) outliers start: 47 outliers final: 21 residues processed: 232 average time/residue: 0.0802 time to fit residues: 27.2979 Evaluate side-chains 174 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 114 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.233769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.202858 restraints weight = 14854.071| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 3.42 r_work: 0.4285 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10214 Z= 0.160 Angle : 0.715 9.589 13860 Z= 0.382 Chirality : 0.045 0.172 1538 Planarity : 0.006 0.070 1686 Dihedral : 7.435 58.638 1340 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.18 % Allowed : 18.59 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -3.74 (0.22), residues: 1168 helix: -2.18 (0.17), residues: 718 sheet: -3.34 (0.78), residues: 26 loop : -2.72 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 478 TYR 0.030 0.001 TYR A 323 PHE 0.031 0.002 PHE A 461 TRP 0.034 0.002 TRP A 629 HIS 0.007 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (10206) covalent geometry : angle 0.71376 / 0.38 (13844) SS BOND : bond 0.00448 / 0.19 ( 8) SS BOND : angle 1.36232 / 0.68 ( 16) hydrogen bonds : bond 0.06054 / 3.95 ( 418) hydrogen bonds : angle 6.68983 / 4.66 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6319 (OUTLIER) cc_final: 0.5045 (t-90) REVERT: A 298 ILE cc_start: 0.7936 (tp) cc_final: 0.7573 (tt) REVERT: A 403 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 555 MET cc_start: 0.8102 (tpp) cc_final: 0.7826 (tpp) REVERT: A 586 TYR cc_start: 0.5158 (OUTLIER) cc_final: 0.3713 (t80) REVERT: A 588 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5612 (mm) REVERT: A 590 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.3849 (mppt) REVERT: A 595 GLU cc_start: 0.6710 (mp0) cc_final: 0.6250 (mp0) REVERT: A 742 MET cc_start: 0.7751 (mmt) cc_final: 0.7531 (tpp) REVERT: B 101 TYR cc_start: 0.6162 (t80) cc_final: 0.5884 (t80) REVERT: B 275 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.5015 (t-90) REVERT: B 298 ILE cc_start: 0.7981 (tp) cc_final: 0.7645 (tt) REVERT: B 403 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7488 (tm-30) REVERT: B 586 TYR cc_start: 0.4953 (OUTLIER) cc_final: 0.4087 (t80) REVERT: B 590 LYS cc_start: 0.5190 (OUTLIER) cc_final: 0.3640 (mppt) REVERT: B 730 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7546 (mt0) outliers start: 45 outliers final: 26 residues processed: 207 average time/residue: 0.0794 time to fit residues: 24.6173 Evaluate side-chains 179 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.233091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.201498 restraints weight = 15096.907| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 3.46 r_work: 0.4271 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10214 Z= 0.163 Angle : 0.691 12.841 13860 Z= 0.368 Chirality : 0.045 0.173 1538 Planarity : 0.006 0.072 1686 Dihedral : 7.152 57.979 1340 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.46 % Allowed : 22.21 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -3.28 (0.23), residues: 1168 helix: -1.79 (0.17), residues: 720 sheet: -3.46 (0.74), residues: 26 loop : -2.54 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 753 TYR 0.027 0.001 TYR A 323 PHE 0.029 0.002 PHE B 461 TRP 0.035 0.002 TRP A 629 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (10206) covalent geometry : angle 0.68987 / 0.37 (13844) SS BOND : bond 0.00248 / 0.11 ( 8) SS BOND : angle 1.27229 / 0.63 ( 16) hydrogen bonds : bond 0.05709 / 3.73 ( 418) hydrogen bonds : angle 6.41624 / 4.46 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.5042 (t-90) REVERT: A 298 ILE cc_start: 0.8013 (tp) cc_final: 0.7684 (tt) REVERT: A 377 PHE cc_start: 0.3717 (OUTLIER) cc_final: 0.3404 (t80) REVERT: A 403 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 586 TYR cc_start: 0.5097 (OUTLIER) cc_final: 0.3880 (t80) REVERT: A 588 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5563 (mm) REVERT: A 595 GLU cc_start: 0.6673 (mp0) cc_final: 0.6253 (mp0) REVERT: A 857 ILE cc_start: 0.7161 (tp) cc_final: 0.6950 (tt) REVERT: B 101 TYR cc_start: 0.6154 (t80) cc_final: 0.5866 (t80) REVERT: B 270 TYR cc_start: 0.4878 (t80) cc_final: 0.4632 (t80) REVERT: B 298 ILE cc_start: 0.8114 (tp) cc_final: 0.7786 (tt) REVERT: B 394 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7519 (mm) REVERT: B 403 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7418 (tm-30) REVERT: B 586 TYR cc_start: 0.4988 (OUTLIER) cc_final: 0.4040 (t80) REVERT: B 730 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: B 768 HIS cc_start: 0.4645 (t-90) cc_final: 0.4365 (t-90) outliers start: 48 outliers final: 27 residues processed: 203 average time/residue: 0.0720 time to fit residues: 22.4262 Evaluate side-chains 180 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 730 GLN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 52 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 60 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.234319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.203469 restraints weight = 15093.520| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 3.49 r_work: 0.4288 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10214 Z= 0.147 Angle : 0.685 12.870 13860 Z= 0.356 Chirality : 0.044 0.165 1538 Planarity : 0.006 0.071 1686 Dihedral : 6.810 56.331 1332 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.83 % Allowed : 22.40 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.89 (0.23), residues: 1168 helix: -1.47 (0.18), residues: 718 sheet: -3.37 (0.75), residues: 26 loop : -2.41 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 753 TYR 0.025 0.001 TYR A 323 PHE 0.019 0.002 PHE B 461 TRP 0.032 0.002 TRP B 273 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (10206) covalent geometry : angle 0.68385 / 0.36 (13844) SS BOND : bond 0.00190 / 0.09 ( 8) SS BOND : angle 1.28547 / 0.64 ( 16) hydrogen bonds : bond 0.05361 / 3.52 ( 418) hydrogen bonds : angle 6.22573 / 4.32 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6494 (OUTLIER) cc_final: 0.5217 (t-90) REVERT: A 298 ILE cc_start: 0.8000 (tp) cc_final: 0.7662 (tt) REVERT: A 377 PHE cc_start: 0.3519 (OUTLIER) cc_final: 0.3235 (t80) REVERT: A 403 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 586 TYR cc_start: 0.5075 (OUTLIER) cc_final: 0.3893 (t80) REVERT: A 595 GLU cc_start: 0.6633 (mp0) cc_final: 0.6241 (mp0) REVERT: B 101 TYR cc_start: 0.6228 (t80) cc_final: 0.5897 (t80) REVERT: B 138 TYR cc_start: 0.5177 (m-80) cc_final: 0.4890 (m-80) REVERT: B 298 ILE cc_start: 0.8034 (tp) cc_final: 0.7665 (tt) REVERT: B 394 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7518 (mm) REVERT: B 403 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 565 SER cc_start: 0.7397 (OUTLIER) cc_final: 0.6927 (p) REVERT: B 586 TYR cc_start: 0.4989 (OUTLIER) cc_final: 0.4099 (t80) REVERT: B 742 MET cc_start: 0.7873 (tpp) cc_final: 0.7399 (mmt) REVERT: B 768 HIS cc_start: 0.4506 (t-90) cc_final: 0.4234 (t-90) outliers start: 52 outliers final: 36 residues processed: 205 average time/residue: 0.0653 time to fit residues: 20.5260 Evaluate side-chains 193 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.234150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.203043 restraints weight = 15068.786| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 3.49 r_work: 0.4285 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10214 Z= 0.154 Angle : 0.676 10.260 13860 Z= 0.352 Chirality : 0.044 0.165 1538 Planarity : 0.005 0.070 1686 Dihedral : 6.585 54.379 1330 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.67 % Allowed : 22.77 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.65 (0.24), residues: 1168 helix: -1.23 (0.18), residues: 716 sheet: -3.42 (0.74), residues: 26 loop : -2.38 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 701 TYR 0.026 0.001 TYR A 528 PHE 0.017 0.002 PHE B 382 TRP 0.032 0.002 TRP B 629 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (10206) covalent geometry : angle 0.67496 / 0.35 (13844) SS BOND : bond 0.00319 / 0.15 ( 8) SS BOND : angle 1.23548 / 0.62 ( 16) hydrogen bonds : bond 0.05343 / 3.51 ( 418) hydrogen bonds : angle 6.11682 / 4.24 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 164 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.5383 (t-90) REVERT: A 298 ILE cc_start: 0.8014 (tp) cc_final: 0.7681 (tt) REVERT: A 377 PHE cc_start: 0.3431 (OUTLIER) cc_final: 0.3145 (t80) REVERT: A 586 TYR cc_start: 0.5096 (OUTLIER) cc_final: 0.3941 (t80) REVERT: A 595 GLU cc_start: 0.6597 (mp0) cc_final: 0.6235 (mp0) REVERT: A 666 TYR cc_start: 0.8820 (m-10) cc_final: 0.8569 (m-80) REVERT: A 730 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7340 (mp10) REVERT: B 101 TYR cc_start: 0.6317 (t80) cc_final: 0.5970 (t80) REVERT: B 138 TYR cc_start: 0.5116 (m-80) cc_final: 0.4856 (m-80) REVERT: B 298 ILE cc_start: 0.8028 (tp) cc_final: 0.7663 (tt) REVERT: B 394 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7592 (mm) REVERT: B 403 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 507 MET cc_start: 0.8415 (ppp) cc_final: 0.7791 (ptt) REVERT: B 565 SER cc_start: 0.7378 (OUTLIER) cc_final: 0.6914 (p) REVERT: B 586 TYR cc_start: 0.4958 (OUTLIER) cc_final: 0.4034 (t80) REVERT: B 742 MET cc_start: 0.8025 (tpp) cc_final: 0.7628 (mmt) REVERT: B 768 HIS cc_start: 0.4512 (t-90) cc_final: 0.4209 (t-90) outliers start: 61 outliers final: 42 residues processed: 211 average time/residue: 0.0732 time to fit residues: 23.8044 Evaluate side-chains 198 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 63 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 79 optimal weight: 0.0570 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.236142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.206196 restraints weight = 15092.918| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 3.33 r_work: 0.4334 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10214 Z= 0.149 Angle : 0.677 13.705 13860 Z= 0.351 Chirality : 0.044 0.163 1538 Planarity : 0.006 0.069 1686 Dihedral : 6.448 52.616 1330 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.93 % Allowed : 23.88 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.40 (0.24), residues: 1168 helix: -1.00 (0.19), residues: 704 sheet: -3.35 (0.75), residues: 26 loop : -2.35 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 753 TYR 0.035 0.001 TYR A 528 PHE 0.017 0.002 PHE B 382 TRP 0.041 0.002 TRP A 629 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (10206) covalent geometry : angle 0.67554 / 0.35 (13844) SS BOND : bond 0.00335 / 0.15 ( 8) SS BOND : angle 1.26871 / 0.65 ( 16) hydrogen bonds : bond 0.05183 / 3.43 ( 418) hydrogen bonds : angle 5.97650 / 4.15 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 167 time to evaluate : 0.258 Fit side-chains REVERT: A 275 HIS cc_start: 0.6343 (OUTLIER) cc_final: 0.5588 (t-90) REVERT: A 298 ILE cc_start: 0.7910 (tp) cc_final: 0.7560 (tt) REVERT: A 377 PHE cc_start: 0.3295 (OUTLIER) cc_final: 0.2959 (t80) REVERT: A 586 TYR cc_start: 0.5084 (OUTLIER) cc_final: 0.4035 (t80) REVERT: A 595 GLU cc_start: 0.6571 (mp0) cc_final: 0.6237 (mp0) REVERT: A 629 TRP cc_start: 0.5578 (m-90) cc_final: 0.5234 (m-90) REVERT: A 730 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7360 (mp10) REVERT: B 138 TYR cc_start: 0.5286 (m-80) cc_final: 0.4863 (m-80) REVERT: B 298 ILE cc_start: 0.7995 (tp) cc_final: 0.7650 (tt) REVERT: B 394 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7592 (mm) REVERT: B 507 MET cc_start: 0.8254 (ppp) cc_final: 0.7674 (ptt) REVERT: B 565 SER cc_start: 0.7220 (OUTLIER) cc_final: 0.6913 (p) REVERT: B 586 TYR cc_start: 0.4951 (OUTLIER) cc_final: 0.4044 (t80) REVERT: B 742 MET cc_start: 0.8093 (tpp) cc_final: 0.7687 (mmt) REVERT: B 768 HIS cc_start: 0.4343 (t-90) cc_final: 0.4116 (t-90) outliers start: 53 outliers final: 39 residues processed: 209 average time/residue: 0.0784 time to fit residues: 24.5234 Evaluate side-chains 197 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 0.0020 chunk 85 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN B 308 GLN B 726 GLN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.237543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.208368 restraints weight = 15087.433| |-----------------------------------------------------------------------------| r_work (start): 0.4558 rms_B_bonded: 3.26 r_work: 0.4332 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10214 Z= 0.150 Angle : 0.694 15.325 13860 Z= 0.356 Chirality : 0.044 0.161 1538 Planarity : 0.006 0.067 1686 Dihedral : 6.214 50.999 1328 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 4.93 % Allowed : 23.98 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.26 (0.24), residues: 1168 helix: -0.87 (0.19), residues: 714 sheet: -3.26 (0.76), residues: 26 loop : -2.35 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 753 TYR 0.041 0.002 TYR B 528 PHE 0.022 0.001 PHE B 558 TRP 0.036 0.002 TRP B 629 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (10206) covalent geometry : angle 0.69273 / 0.36 (13844) SS BOND : bond 0.00512 / 0.25 ( 8) SS BOND : angle 1.32180 / 0.67 ( 16) hydrogen bonds : bond 0.05104 / 3.37 ( 418) hydrogen bonds : angle 5.90926 / 4.10 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6313 (OUTLIER) cc_final: 0.5888 (t-90) REVERT: A 298 ILE cc_start: 0.7934 (tp) cc_final: 0.7592 (tt) REVERT: A 377 PHE cc_start: 0.3002 (OUTLIER) cc_final: 0.2715 (t80) REVERT: A 586 TYR cc_start: 0.4879 (OUTLIER) cc_final: 0.3862 (t80) REVERT: A 595 GLU cc_start: 0.6577 (mp0) cc_final: 0.6244 (mp0) REVERT: A 730 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7378 (mp10) REVERT: A 753 ARG cc_start: 0.6346 (mtt-85) cc_final: 0.6097 (ptm160) REVERT: A 773 MET cc_start: 0.6858 (mmt) cc_final: 0.6614 (mmt) REVERT: B 138 TYR cc_start: 0.5225 (m-80) cc_final: 0.4807 (m-80) REVERT: B 298 ILE cc_start: 0.7950 (tp) cc_final: 0.7555 (tt) REVERT: B 394 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7620 (mm) REVERT: B 507 MET cc_start: 0.8105 (ppp) cc_final: 0.7660 (ptt) REVERT: B 565 SER cc_start: 0.7109 (OUTLIER) cc_final: 0.6846 (p) REVERT: B 586 TYR cc_start: 0.4922 (OUTLIER) cc_final: 0.4073 (t80) REVERT: B 730 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7499 (mp10) REVERT: B 742 MET cc_start: 0.8049 (tpp) cc_final: 0.7653 (mmt) REVERT: B 768 HIS cc_start: 0.4405 (t-90) cc_final: 0.4140 (t-90) outliers start: 53 outliers final: 41 residues processed: 207 average time/residue: 0.0752 time to fit residues: 23.2905 Evaluate side-chains 201 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.235042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.205006 restraints weight = 14997.362| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 3.29 r_work: 0.4298 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10214 Z= 0.173 Angle : 0.722 16.461 13860 Z= 0.371 Chirality : 0.045 0.219 1538 Planarity : 0.006 0.068 1686 Dihedral : 6.287 50.097 1328 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.93 % Allowed : 24.63 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.26 (0.24), residues: 1168 helix: -0.83 (0.19), residues: 702 sheet: -3.37 (0.74), residues: 26 loop : -2.37 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 753 TYR 0.026 0.001 TYR A 528 PHE 0.030 0.002 PHE A 556 TRP 0.047 0.002 TRP A 629 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (10206) covalent geometry : angle 0.72126 / 0.37 (13844) SS BOND : bond 0.00326 / 0.16 ( 8) SS BOND : angle 1.33759 / 0.67 ( 16) hydrogen bonds : bond 0.05398 / 3.57 ( 418) hydrogen bonds : angle 5.95418 / 4.12 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 275 HIS cc_start: 0.6272 (OUTLIER) cc_final: 0.5949 (t-90) REVERT: A 298 ILE cc_start: 0.7995 (tp) cc_final: 0.7639 (tt) REVERT: A 377 PHE cc_start: 0.3242 (OUTLIER) cc_final: 0.2982 (t80) REVERT: A 524 LEU cc_start: 0.8073 (tt) cc_final: 0.7848 (pp) REVERT: A 586 TYR cc_start: 0.4985 (OUTLIER) cc_final: 0.3939 (t80) REVERT: A 595 GLU cc_start: 0.6648 (mp0) cc_final: 0.6305 (mp0) REVERT: A 629 TRP cc_start: 0.5847 (m-90) cc_final: 0.5539 (m-90) REVERT: A 730 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7458 (mp10) REVERT: B 101 TYR cc_start: 0.7213 (m-80) cc_final: 0.7007 (m-80) REVERT: B 138 TYR cc_start: 0.5232 (m-80) cc_final: 0.4790 (m-80) REVERT: B 298 ILE cc_start: 0.8037 (tp) cc_final: 0.7675 (tt) REVERT: B 394 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7648 (mm) REVERT: B 507 MET cc_start: 0.8121 (ppp) cc_final: 0.7708 (ptt) REVERT: B 565 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.7050 (p) REVERT: B 586 TYR cc_start: 0.4889 (OUTLIER) cc_final: 0.3992 (t80) REVERT: B 714 MET cc_start: 0.6238 (mmt) cc_final: 0.5919 (mmm) REVERT: B 730 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7603 (mp10) REVERT: B 742 MET cc_start: 0.8219 (tpp) cc_final: 0.7812 (mmt) outliers start: 53 outliers final: 43 residues processed: 197 average time/residue: 0.0734 time to fit residues: 22.0174 Evaluate side-chains 197 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 601 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 711 PHE Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.236397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.206435 restraints weight = 14935.778| |-----------------------------------------------------------------------------| r_work (start): 0.4552 rms_B_bonded: 3.32 r_work: 0.4325 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10214 Z= 0.155 Angle : 0.707 14.822 13860 Z= 0.362 Chirality : 0.045 0.215 1538 Planarity : 0.005 0.068 1686 Dihedral : 6.209 49.753 1328 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.46 % Allowed : 24.81 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.22 (0.24), residues: 1168 helix: -0.71 (0.19), residues: 692 sheet: -3.26 (0.76), residues: 26 loop : -2.51 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 478 TYR 0.028 0.001 TYR A 569 PHE 0.032 0.002 PHE A 556 TRP 0.042 0.002 TRP A 629 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (10206) covalent geometry : angle 0.70583 / 0.36 (13844) SS BOND : bond 0.00331 / 0.17 ( 8) SS BOND : angle 1.32385 / 0.68 ( 16) hydrogen bonds : bond 0.05147 / 3.42 ( 418) hydrogen bonds : angle 5.87462 / 4.07 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 101 TYR cc_start: 0.6820 (m-80) cc_final: 0.6335 (m-80) REVERT: A 298 ILE cc_start: 0.7971 (tp) cc_final: 0.7597 (tt) REVERT: A 586 TYR cc_start: 0.4852 (OUTLIER) cc_final: 0.3879 (t80) REVERT: A 595 GLU cc_start: 0.6633 (mp0) cc_final: 0.6317 (mp0) REVERT: A 629 TRP cc_start: 0.5897 (m-90) cc_final: 0.5585 (m-90) REVERT: A 730 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7420 (mp10) REVERT: B 138 TYR cc_start: 0.5370 (m-80) cc_final: 0.4961 (m-80) REVERT: B 298 ILE cc_start: 0.8002 (tp) cc_final: 0.7631 (tt) REVERT: B 394 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7662 (mm) REVERT: B 507 MET cc_start: 0.8042 (ppp) cc_final: 0.7727 (ptt) REVERT: B 565 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.7042 (p) REVERT: B 573 PHE cc_start: 0.7759 (t80) cc_final: 0.7532 (t80) REVERT: B 586 TYR cc_start: 0.4803 (OUTLIER) cc_final: 0.3884 (t80) REVERT: B 730 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7486 (mp10) REVERT: B 742 MET cc_start: 0.8165 (tpp) cc_final: 0.7763 (mmt) outliers start: 48 outliers final: 37 residues processed: 195 average time/residue: 0.0711 time to fit residues: 21.1268 Evaluate side-chains 193 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 668 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 586 TYR Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 668 TYR Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 729 MET Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.232533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.201824 restraints weight = 15028.840| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 3.18 r_work: 0.4280 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10214 Z= 0.198 Angle : 0.743 14.299 13860 Z= 0.387 Chirality : 0.046 0.159 1538 Planarity : 0.006 0.076 1686 Dihedral : 6.212 45.057 1326 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 4.18 % Allowed : 25.65 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.45 (0.24), residues: 1168 helix: -0.90 (0.19), residues: 712 sheet: -3.49 (0.74), residues: 26 loop : -2.66 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 289 TYR 0.028 0.002 TYR A 569 PHE 0.040 0.002 PHE A 573 TRP 0.044 0.003 TRP A 629 HIS 0.004 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (10206) covalent geometry : angle 0.74239 / 0.39 (13844) SS BOND : bond 0.00379 / 0.19 ( 8) SS BOND : angle 1.36390 / 0.69 ( 16) hydrogen bonds : bond 0.05669 / 3.74 ( 418) hydrogen bonds : angle 6.02051 / 4.16 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.99 seconds wall clock time: 40 minutes 39.38 seconds (2439.38 seconds total)