Starting phenix.real_space_refine on Sat Oct 11 12:37:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w7l_37340/10_2025/8w7l_37340.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w7l_37340/10_2025/8w7l_37340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w7l_37340/10_2025/8w7l_37340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w7l_37340/10_2025/8w7l_37340.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w7l_37340/10_2025/8w7l_37340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w7l_37340/10_2025/8w7l_37340.map" } resolution = 3.75 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= 0.031 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 P 2 5.49 5 S 32 5.16 5 C 9440 2.51 5 N 2416 2.21 5 O 2746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14636 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 7072 Classifications: {'peptide': 865} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 836} Chain: "C" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 241 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 7072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 865, 7072 Classifications: {'peptide': 865} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 836} Chain: "D" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 241 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.36, per 1000 atoms: 0.23 Number of scatterers: 14636 At special positions: 0 Unit cell: (115.54, 128.26, 102.82, 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) S 32 16.00 P 2 15.00 O 2746 8.00 N 2416 7.00 C 9440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 636.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 12 sheets defined 38.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 68 through 80 Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.735A pdb=" N LEU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 removed outlier: 3.527A pdb=" N LYS A 264 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 326 through 345 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 399 through 417 Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.918A pdb=" N THR A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 463 removed outlier: 3.704A pdb=" N ILE A 451 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 512 removed outlier: 3.987A pdb=" N PHE A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.987A pdb=" N LEU A 526 " --> pdb=" O TYR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 550 removed outlier: 4.327A pdb=" N LEU A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 removed outlier: 3.735A pdb=" N ILE A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 571 " --> pdb=" O ASN A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.529A pdb=" N GLU A 594 " --> pdb=" O TRP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 609 removed outlier: 3.896A pdb=" N ALA A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 613 removed outlier: 3.540A pdb=" N PHE A 613 " --> pdb=" O ILE A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 610 through 613' Processing helix chain 'A' and resid 625 through 639 removed outlier: 3.658A pdb=" N VAL A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 662 removed outlier: 3.674A pdb=" N ASN A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 660 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 667 removed outlier: 3.766A pdb=" N THR A 666 " --> pdb=" O ASN A 663 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A 667 " --> pdb=" O PRO A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 667' Processing helix chain 'A' and resid 690 through 705 removed outlier: 4.128A pdb=" N VAL A 694 " --> pdb=" O GLY A 690 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 703 " --> pdb=" O GLY A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 removed outlier: 3.557A pdb=" N LYS A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 removed outlier: 4.161A pdb=" N LEU A 752 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 778 removed outlier: 3.934A pdb=" N TYR A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU A 771 " --> pdb=" O TYR A 767 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR A 772 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 799 removed outlier: 3.876A pdb=" N GLU A 796 " --> pdb=" O PHE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 820 removed outlier: 3.874A pdb=" N GLU A 817 " --> pdb=" O LYS A 813 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 818 " --> pdb=" O LYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 860 removed outlier: 4.342A pdb=" N GLY A 854 " --> pdb=" O GLY A 850 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.879A pdb=" N THR C 18 " --> pdb=" O GLN C 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 93 through 99 Processing helix chain 'B' and resid 122 through 134 removed outlier: 3.731A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.540A pdb=" N LYS B 264 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 326 through 345 Processing helix chain 'B' and resid 399 through 417 Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.911A pdb=" N THR B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 435 " --> pdb=" O SER B 431 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 463 removed outlier: 3.714A pdb=" N ILE B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 512 removed outlier: 3.987A pdb=" N PHE B 495 " --> pdb=" O ASP B 491 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 550 removed outlier: 3.688A pdb=" N LEU B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 546 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 572 removed outlier: 4.001A pdb=" N ILE B 566 " --> pdb=" O ARG B 562 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 594 removed outlier: 4.273A pdb=" N THR B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 589 " --> pdb=" O LYS B 585 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 609 removed outlier: 3.991A pdb=" N ALA B 601 " --> pdb=" O GLU B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 613 removed outlier: 3.514A pdb=" N PHE B 613 " --> pdb=" O ILE B 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 610 through 613' Processing helix chain 'B' and resid 625 through 639 removed outlier: 3.542A pdb=" N VAL B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 662 removed outlier: 3.549A pdb=" N ASN B 659 " --> pdb=" O GLU B 655 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR B 660 " --> pdb=" O TYR B 656 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 667 removed outlier: 3.799A pdb=" N THR B 666 " --> pdb=" O ASN B 663 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE B 667 " --> pdb=" O PRO B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 663 through 667' Processing helix chain 'B' and resid 690 through 706 removed outlier: 4.080A pdb=" N VAL B 694 " --> pdb=" O GLY B 690 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 703 " --> pdb=" O GLY B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 722 removed outlier: 3.526A pdb=" N LYS B 711 " --> pdb=" O GLU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 759 removed outlier: 4.134A pdb=" N LEU B 752 " --> pdb=" O GLY B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 769 Processing helix chain 'B' and resid 769 through 778 removed outlier: 4.552A pdb=" N SER B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 799 removed outlier: 3.876A pdb=" N GLU B 796 " --> pdb=" O PHE B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 820 removed outlier: 3.860A pdb=" N GLU B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 818 " --> pdb=" O LYS B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 860 removed outlier: 4.346A pdb=" N GLY B 854 " --> pdb=" O GLY B 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 removed outlier: 3.698A pdb=" N THR D 18 " --> pdb=" O GLN D 14 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 225 removed outlier: 5.073A pdb=" N ILE A 219 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG A 235 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 221 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 231 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 248 removed outlier: 6.108A pdb=" N HIS A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS A 289 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE A 295 " --> pdb=" O HIS A 287 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS A 287 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY A 297 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA6, first strand: chain 'A' and resid 823 through 826 Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.906A pdb=" N GLY B 57 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 157 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 225 removed outlier: 5.024A pdb=" N ILE B 219 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG B 235 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN B 221 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE B 231 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 243 through 248 removed outlier: 5.987A pdb=" N HIS B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS B 289 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE B 295 " --> pdb=" O HIS B 287 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS B 287 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLY B 297 " --> pdb=" O TYR B 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AB3, first strand: chain 'B' and resid 823 through 826 465 hydrogen bonds defined for protein. 1368 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: 2.11 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2466 1.30 - 1.43: 4009 1.43 - 1.56: 8440 1.56 - 1.68: 17 1.68 - 1.81: 48 Bond restraints: 14980 Sorted by residual: bond pdb=" CA ASP D 22 " pdb=" C ASP D 22 " ideal model delta sigma weight residual 1.522 1.402 0.120 1.27e-02 6.20e+03 8.99e+01 bond pdb=" CA ASP C 22 " pdb=" C ASP C 22 " ideal model delta sigma weight residual 1.522 1.407 0.115 1.24e-02 6.50e+03 8.60e+01 bond pdb=" C ASP C 22 " pdb=" O ASP C 22 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.24e-02 6.50e+03 2.55e+01 bond pdb=" C ASP D 22 " pdb=" O ASP D 22 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.29e-02 6.01e+03 2.39e+01 bond pdb=" CA THR A 747 " pdb=" CB THR A 747 " ideal model delta sigma weight residual 1.527 1.636 -0.109 2.48e-02 1.63e+03 1.92e+01 ... (remaining 14975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 20101 4.91 - 9.83: 149 9.83 - 14.74: 24 14.74 - 19.66: 1 19.66 - 24.57: 3 Bond angle restraints: 20278 Sorted by residual: angle pdb=" N PHE D 26 " pdb=" CA PHE D 26 " pdb=" C PHE D 26 " ideal model delta sigma weight residual 107.20 131.77 -24.57 1.70e+00 3.46e-01 2.09e+02 angle pdb=" N PHE C 26 " pdb=" CA PHE C 26 " pdb=" C PHE C 26 " ideal model delta sigma weight residual 107.20 130.86 -23.66 1.70e+00 3.46e-01 1.94e+02 angle pdb=" N GLY C 23 " pdb=" CA GLY C 23 " pdb=" C GLY C 23 " ideal model delta sigma weight residual 113.18 133.43 -20.25 2.37e+00 1.78e-01 7.30e+01 angle pdb=" N GLY D 23 " pdb=" CA GLY D 23 " pdb=" C GLY D 23 " ideal model delta sigma weight residual 113.18 132.09 -18.91 2.37e+00 1.78e-01 6.37e+01 angle pdb=" C PHE B 553 " pdb=" N LYS B 554 " pdb=" CA LYS B 554 " ideal model delta sigma weight residual 121.54 136.04 -14.50 1.91e+00 2.74e-01 5.77e+01 ... (remaining 20273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 7768 17.40 - 34.81: 887 34.81 - 52.21: 168 52.21 - 69.61: 15 69.61 - 87.02: 22 Dihedral angle restraints: 8860 sinusoidal: 3566 harmonic: 5294 Sorted by residual: dihedral pdb=" CA SER A 732 " pdb=" C SER A 732 " pdb=" N LEU A 733 " pdb=" CA LEU A 733 " ideal model delta harmonic sigma weight residual -180.00 -144.59 -35.41 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" N ARG D 25 " pdb=" C ARG D 25 " pdb=" CA ARG D 25 " pdb=" CB ARG D 25 " ideal model delta harmonic sigma weight residual 122.80 139.95 -17.15 0 2.50e+00 1.60e-01 4.70e+01 dihedral pdb=" C ARG D 25 " pdb=" N ARG D 25 " pdb=" CA ARG D 25 " pdb=" CB ARG D 25 " ideal model delta harmonic sigma weight residual -122.60 -139.28 16.68 0 2.50e+00 1.60e-01 4.45e+01 ... (remaining 8857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2135 0.156 - 0.311: 48 0.311 - 0.467: 3 0.467 - 0.623: 2 0.623 - 0.778: 2 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA ARG D 25 " pdb=" N ARG D 25 " pdb=" C ARG D 25 " pdb=" CB ARG D 25 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CA ARG C 25 " pdb=" N ARG C 25 " pdb=" C ARG C 25 " pdb=" CB ARG C 25 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CA PHE D 26 " pdb=" N PHE D 26 " pdb=" C PHE D 26 " pdb=" CB PHE D 26 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.34e+00 ... (remaining 2187 not shown) Planarity restraints: 2598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 21 " -0.039 2.00e-02 2.50e+03 7.96e-02 6.33e+01 pdb=" C VAL C 21 " 0.137 2.00e-02 2.50e+03 pdb=" O VAL C 21 " -0.055 2.00e-02 2.50e+03 pdb=" N ASP C 22 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 21 " -0.037 2.00e-02 2.50e+03 7.63e-02 5.83e+01 pdb=" C VAL D 21 " 0.132 2.00e-02 2.50e+03 pdb=" O VAL D 21 " -0.053 2.00e-02 2.50e+03 pdb=" N ASP D 22 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 503 " 0.021 2.00e-02 2.50e+03 2.50e-02 1.10e+01 pdb=" CG PHE B 503 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE B 503 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 503 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE B 503 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 503 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 503 " 0.005 2.00e-02 2.50e+03 ... (remaining 2595 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4192 2.81 - 3.34: 13565 3.34 - 3.86: 24427 3.86 - 4.38: 27809 4.38 - 4.90: 46168 Nonbonded interactions: 116161 Sorted by model distance: nonbonded pdb=" OE2 GLU A 121 " pdb=" OG SER A 124 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR B 232 " pdb=" O LEU B 245 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 429 " pdb=" O ARG A 821 " model vdw 2.299 3.040 nonbonded pdb=" OE2 GLU A 335 " pdb=" OH TYR A 453 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR B 429 " pdb=" O ARG B 821 " model vdw 2.312 3.040 ... (remaining 116156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.650 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.005 0.120 14980 Z= 0.287 Angle : 1.154 24.573 20278 Z= 0.608 Chirality : 0.067 0.778 2190 Planarity : 0.006 0.080 2598 Dihedral : 15.254 87.018 5472 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.83 % Allowed : 13.29 % Favored : 85.88 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.23 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -3.90 (0.16), residues: 1806 helix: -1.90 (0.16), residues: 652 sheet: -1.55 (0.54), residues: 112 loop : -3.33 (0.16), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.035 0.002 TYR A 558 PHE 0.058 0.002 PHE B 503 TRP 0.036 0.002 TRP A 43 HIS 0.011 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00523 (14980) covalent geometry : angle 1.15413 (20278) hydrogen bonds : bond 0.15879 ( 465) hydrogen bonds : angle 7.41828 ( 1368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.9045 (mm) cc_final: 0.8420 (tp) REVERT: A 199 ASP cc_start: 0.7379 (p0) cc_final: 0.7161 (p0) REVERT: A 291 TRP cc_start: 0.8486 (t60) cc_final: 0.7727 (t60) REVERT: A 333 ILE cc_start: 0.9143 (pt) cc_final: 0.8907 (pt) REVERT: A 353 ASP cc_start: 0.7400 (t0) cc_final: 0.7158 (t0) REVERT: A 355 HIS cc_start: 0.8207 (p90) cc_final: 0.7939 (p-80) REVERT: A 405 TRP cc_start: 0.7411 (m100) cc_final: 0.7127 (m100) REVERT: A 481 HIS cc_start: 0.8391 (p-80) cc_final: 0.8057 (p-80) REVERT: A 559 TYR cc_start: 0.8091 (m-10) cc_final: 0.7866 (m-10) REVERT: A 862 LYS cc_start: 0.8720 (pptt) cc_final: 0.8107 (tmtt) REVERT: C 16 ASP cc_start: 0.8105 (p0) cc_final: 0.7879 (p0) REVERT: B 73 LEU cc_start: 0.8466 (tp) cc_final: 0.8107 (tt) REVERT: B 79 ILE cc_start: 0.8854 (mm) cc_final: 0.8553 (tp) REVERT: B 333 ILE cc_start: 0.9124 (pt) cc_final: 0.8896 (pt) REVERT: B 353 ASP cc_start: 0.7380 (t0) cc_final: 0.7143 (t0) REVERT: B 355 HIS cc_start: 0.8197 (p90) cc_final: 0.7944 (p-80) REVERT: B 405 TRP cc_start: 0.7465 (m100) cc_final: 0.7168 (m100) REVERT: B 417 MET cc_start: 0.8916 (tpp) cc_final: 0.8650 (tpt) REVERT: B 494 ASP cc_start: 0.7928 (p0) cc_final: 0.7709 (p0) REVERT: B 862 LYS cc_start: 0.8731 (pptt) cc_final: 0.8019 (tmtt) REVERT: B 864 THR cc_start: 0.8433 (p) cc_final: 0.8194 (p) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.1146 time to fit residues: 49.5806 Evaluate side-chains 176 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 287 HIS A 345 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 470 ASN A 676 GLN A 731 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 81 HIS B 287 HIS B 345 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 470 ASN B 676 GLN B 731 ASN ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.124649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095612 restraints weight = 35561.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098835 restraints weight = 19326.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.100901 restraints weight = 13416.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.102216 restraints weight = 10732.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.102951 restraints weight = 9361.659| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14980 Z= 0.230 Angle : 0.746 10.209 20278 Z= 0.393 Chirality : 0.047 0.212 2190 Planarity : 0.005 0.053 2598 Dihedral : 6.009 32.656 1974 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.66 % Allowed : 12.62 % Favored : 86.71 % Rotamer: Outliers : 1.60 % Allowed : 13.68 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -3.07 (0.18), residues: 1806 helix: -0.54 (0.19), residues: 686 sheet: -2.20 (0.59), residues: 94 loop : -3.27 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 185 TYR 0.029 0.002 TYR B 232 PHE 0.025 0.002 PHE A 344 TRP 0.023 0.002 TRP A 43 HIS 0.010 0.002 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00519 (14980) covalent geometry : angle 0.74574 (20278) hydrogen bonds : bond 0.04026 ( 465) hydrogen bonds : angle 5.16724 ( 1368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8112 (t0) REVERT: A 217 PHE cc_start: 0.8609 (m-80) cc_final: 0.8381 (m-80) REVERT: A 402 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: A 481 HIS cc_start: 0.8571 (p-80) cc_final: 0.8293 (p-80) REVERT: A 559 TYR cc_start: 0.8156 (m-10) cc_final: 0.7929 (m-10) REVERT: A 862 LYS cc_start: 0.8773 (pptt) cc_final: 0.8336 (ptmt) REVERT: B 33 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8010 (t0) REVERT: B 217 PHE cc_start: 0.8590 (m-80) cc_final: 0.8310 (m-80) REVERT: B 402 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: B 544 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: B 702 TYR cc_start: 0.8008 (t80) cc_final: 0.7749 (t80) REVERT: B 862 LYS cc_start: 0.8731 (pptt) cc_final: 0.8269 (ptmt) outliers start: 25 outliers final: 18 residues processed: 219 average time/residue: 0.1143 time to fit residues: 38.3756 Evaluate side-chains 187 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 633 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 14 optimal weight: 0.0670 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 432 GLN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.126558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097727 restraints weight = 35871.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100990 restraints weight = 19369.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103106 restraints weight = 13397.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104446 restraints weight = 10682.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105314 restraints weight = 9293.001| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14980 Z= 0.140 Angle : 0.650 8.819 20278 Z= 0.336 Chirality : 0.044 0.215 2190 Planarity : 0.004 0.053 2598 Dihedral : 5.677 28.125 1974 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.66 % Allowed : 12.02 % Favored : 87.32 % Rotamer: Outliers : 1.66 % Allowed : 17.84 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.19), residues: 1806 helix: -0.09 (0.19), residues: 686 sheet: -1.47 (0.54), residues: 108 loop : -3.23 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.022 0.001 TYR B 232 PHE 0.021 0.001 PHE B 344 TRP 0.014 0.001 TRP A 34 HIS 0.009 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00323 (14980) covalent geometry : angle 0.65025 (20278) hydrogen bonds : bond 0.03338 ( 465) hydrogen bonds : angle 4.83051 ( 1368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 TRP cc_start: 0.8827 (t60) cc_final: 0.8534 (t60) REVERT: A 397 GLU cc_start: 0.8376 (pm20) cc_final: 0.7984 (pm20) REVERT: A 481 HIS cc_start: 0.8501 (p-80) cc_final: 0.8270 (p-80) REVERT: A 814 LYS cc_start: 0.9287 (tppt) cc_final: 0.8953 (ptpt) REVERT: A 862 LYS cc_start: 0.8606 (pptt) cc_final: 0.8239 (ptmt) REVERT: B 30 LEU cc_start: 0.9089 (tp) cc_final: 0.8772 (tp) REVERT: B 217 PHE cc_start: 0.8527 (m-80) cc_final: 0.8193 (m-80) REVERT: B 397 GLU cc_start: 0.8374 (pm20) cc_final: 0.7979 (pm20) REVERT: B 544 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: B 702 TYR cc_start: 0.8048 (t80) cc_final: 0.7783 (t80) REVERT: B 747 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7572 (t) REVERT: B 814 LYS cc_start: 0.9188 (tppt) cc_final: 0.8816 (ptpt) REVERT: B 862 LYS cc_start: 0.8543 (pptt) cc_final: 0.8186 (ptmt) outliers start: 26 outliers final: 12 residues processed: 209 average time/residue: 0.1006 time to fit residues: 33.7392 Evaluate side-chains 177 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 747 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 47 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 108 optimal weight: 0.0270 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 233 ASN B 345 HIS B 358 ASN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 ASN ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.127657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098439 restraints weight = 36035.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101774 restraints weight = 19601.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103939 restraints weight = 13556.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105306 restraints weight = 10812.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106111 restraints weight = 9406.080| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14980 Z= 0.120 Angle : 0.623 8.519 20278 Z= 0.321 Chirality : 0.043 0.202 2190 Planarity : 0.004 0.053 2598 Dihedral : 5.439 30.435 1974 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.35 % Favored : 87.04 % Rotamer: Outliers : 1.79 % Allowed : 20.65 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -2.46 (0.19), residues: 1806 helix: 0.13 (0.19), residues: 690 sheet: -1.35 (0.54), residues: 108 loop : -3.14 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 484 TYR 0.023 0.001 TYR A 66 PHE 0.019 0.001 PHE B 344 TRP 0.012 0.001 TRP A 34 HIS 0.006 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00275 (14980) covalent geometry : angle 0.62293 (20278) hydrogen bonds : bond 0.03084 ( 465) hydrogen bonds : angle 4.64482 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7384 (mp0) cc_final: 0.7093 (mp0) REVERT: A 291 TRP cc_start: 0.8781 (t60) cc_final: 0.8513 (t60) REVERT: A 397 GLU cc_start: 0.8352 (pm20) cc_final: 0.8034 (pm20) REVERT: A 402 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: A 481 HIS cc_start: 0.8526 (p-80) cc_final: 0.8267 (p-80) REVERT: A 653 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9055 (tp) REVERT: A 747 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7270 (t) REVERT: A 814 LYS cc_start: 0.9185 (tppt) cc_final: 0.8924 (tppt) REVERT: A 860 ASP cc_start: 0.8147 (m-30) cc_final: 0.7940 (m-30) REVERT: A 862 LYS cc_start: 0.8559 (pptt) cc_final: 0.8221 (ptmt) REVERT: B 30 LEU cc_start: 0.9126 (tp) cc_final: 0.8817 (tp) REVERT: B 217 PHE cc_start: 0.8505 (m-80) cc_final: 0.8286 (m-80) REVERT: B 259 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8163 (p) REVERT: B 397 GLU cc_start: 0.8360 (pm20) cc_final: 0.8034 (pm20) REVERT: B 402 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: B 747 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7497 (t) REVERT: B 814 LYS cc_start: 0.9131 (tppt) cc_final: 0.8879 (tppt) REVERT: B 862 LYS cc_start: 0.8565 (pptt) cc_final: 0.8259 (ptmt) outliers start: 28 outliers final: 11 residues processed: 215 average time/residue: 0.1054 time to fit residues: 36.0730 Evaluate side-chains 192 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 747 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN A 345 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090348 restraints weight = 36372.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093391 restraints weight = 19743.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095325 restraints weight = 13781.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.096579 restraints weight = 11136.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.097380 restraints weight = 9759.106| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 14980 Z= 0.257 Angle : 0.740 9.326 20278 Z= 0.384 Chirality : 0.048 0.270 2190 Planarity : 0.005 0.062 2598 Dihedral : 5.863 30.638 1974 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.06 % Favored : 85.38 % Rotamer: Outliers : 3.52 % Allowed : 20.72 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -2.57 (0.19), residues: 1806 helix: -0.04 (0.19), residues: 696 sheet: -1.58 (0.52), residues: 108 loop : -3.14 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 155 TYR 0.028 0.002 TYR B 232 PHE 0.021 0.002 PHE A 344 TRP 0.021 0.002 TRP A 34 HIS 0.012 0.002 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00585 (14980) covalent geometry : angle 0.74001 (20278) hydrogen bonds : bond 0.03792 ( 465) hydrogen bonds : angle 4.94192 ( 1368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8508 (pm20) cc_final: 0.8118 (pm20) REVERT: A 402 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: A 653 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9015 (tp) REVERT: A 702 TYR cc_start: 0.8266 (t80) cc_final: 0.7995 (t80) REVERT: A 747 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7688 (t) REVERT: A 862 LYS cc_start: 0.8463 (pptt) cc_final: 0.8103 (ptmt) REVERT: B 30 LEU cc_start: 0.9227 (tp) cc_final: 0.8925 (tp) REVERT: B 259 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8253 (p) REVERT: B 339 ASP cc_start: 0.8657 (m-30) cc_final: 0.8361 (t0) REVERT: B 397 GLU cc_start: 0.8507 (pm20) cc_final: 0.8127 (pm20) REVERT: B 402 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: B 702 TYR cc_start: 0.8221 (t80) cc_final: 0.7797 (t80) REVERT: B 862 LYS cc_start: 0.8502 (pptt) cc_final: 0.8179 (ptmt) outliers start: 55 outliers final: 25 residues processed: 215 average time/residue: 0.0965 time to fit residues: 33.8744 Evaluate side-chains 185 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 0.8980 chunk 112 optimal weight: 0.0170 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B 836 ASN ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096406 restraints weight = 35636.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099722 restraints weight = 18990.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101854 restraints weight = 13059.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103200 restraints weight = 10421.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103997 restraints weight = 9079.822| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14980 Z= 0.121 Angle : 0.648 9.340 20278 Z= 0.328 Chirality : 0.044 0.231 2190 Planarity : 0.004 0.056 2598 Dihedral : 5.465 31.064 1974 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.62 % Favored : 86.82 % Rotamer: Outliers : 2.94 % Allowed : 22.12 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -2.37 (0.19), residues: 1806 helix: 0.16 (0.19), residues: 694 sheet: -1.31 (0.53), residues: 108 loop : -3.06 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.020 0.001 TYR A 232 PHE 0.019 0.001 PHE A 344 TRP 0.012 0.001 TRP A 34 HIS 0.005 0.001 HIS B 413 Details of bonding type rmsd covalent geometry : bond 0.00273 (14980) covalent geometry : angle 0.64769 (20278) hydrogen bonds : bond 0.03060 ( 465) hydrogen bonds : angle 4.55169 ( 1368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: A 291 TRP cc_start: 0.8693 (t60) cc_final: 0.7914 (t60) REVERT: A 339 ASP cc_start: 0.8568 (m-30) cc_final: 0.8298 (t0) REVERT: A 397 GLU cc_start: 0.8446 (pm20) cc_final: 0.8078 (pm20) REVERT: A 402 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: A 439 LYS cc_start: 0.9157 (mttt) cc_final: 0.8888 (mttt) REVERT: A 653 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9015 (tp) REVERT: A 814 LYS cc_start: 0.9349 (tppt) cc_final: 0.9000 (ptpt) REVERT: A 862 LYS cc_start: 0.8521 (pptt) cc_final: 0.8212 (ptmt) REVERT: B 30 LEU cc_start: 0.9133 (tp) cc_final: 0.8829 (tp) REVERT: B 259 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8204 (p) REVERT: B 268 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: B 339 ASP cc_start: 0.8617 (m-30) cc_final: 0.8363 (t0) REVERT: B 397 GLU cc_start: 0.8457 (pm20) cc_final: 0.8073 (pm20) REVERT: B 402 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: B 702 TYR cc_start: 0.8238 (t80) cc_final: 0.8015 (t80) REVERT: B 814 LYS cc_start: 0.9321 (tppt) cc_final: 0.8972 (ptpt) REVERT: B 862 LYS cc_start: 0.8605 (pptt) cc_final: 0.8348 (ptmt) outliers start: 46 outliers final: 21 residues processed: 226 average time/residue: 0.0993 time to fit residues: 36.6319 Evaluate side-chains 201 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 21 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B 836 ASN ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.121672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.091239 restraints weight = 37129.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.094427 restraints weight = 20684.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.096456 restraints weight = 14677.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.097746 restraints weight = 11941.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098529 restraints weight = 10541.999| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14980 Z= 0.201 Angle : 0.705 10.541 20278 Z= 0.359 Chirality : 0.047 0.350 2190 Planarity : 0.004 0.059 2598 Dihedral : 5.560 30.172 1974 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.29 % Favored : 86.16 % Rotamer: Outliers : 3.45 % Allowed : 21.99 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -2.35 (0.19), residues: 1806 helix: 0.21 (0.19), residues: 694 sheet: -1.46 (0.53), residues: 108 loop : -3.05 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 155 TYR 0.024 0.002 TYR A 66 PHE 0.021 0.002 PHE B 217 TRP 0.014 0.002 TRP A 34 HIS 0.008 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00466 (14980) covalent geometry : angle 0.70515 (20278) hydrogen bonds : bond 0.03383 ( 465) hydrogen bonds : angle 4.64629 ( 1368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8644 (m-30) cc_final: 0.8365 (t0) REVERT: A 397 GLU cc_start: 0.8509 (pm20) cc_final: 0.8141 (pm20) REVERT: A 439 LYS cc_start: 0.9180 (mttt) cc_final: 0.8964 (ttmm) REVERT: A 653 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9046 (tp) REVERT: A 702 TYR cc_start: 0.8385 (t80) cc_final: 0.7964 (t80) REVERT: A 862 LYS cc_start: 0.8521 (pptt) cc_final: 0.8211 (ptmt) REVERT: C 17 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 30 LEU cc_start: 0.9214 (tp) cc_final: 0.8919 (tp) REVERT: B 98 MET cc_start: 0.8564 (tmm) cc_final: 0.8289 (tmm) REVERT: B 259 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8259 (p) REVERT: B 397 GLU cc_start: 0.8535 (pm20) cc_final: 0.8164 (pm20) REVERT: B 402 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: B 702 TYR cc_start: 0.8370 (t80) cc_final: 0.8011 (t80) outliers start: 54 outliers final: 34 residues processed: 212 average time/residue: 0.1001 time to fit residues: 34.6864 Evaluate side-chains 193 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain D residue 21 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 21 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A 836 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.124811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.095549 restraints weight = 35966.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.098832 restraints weight = 19080.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100975 restraints weight = 13133.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102298 restraints weight = 10492.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102893 restraints weight = 9160.326| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14980 Z= 0.127 Angle : 0.684 10.354 20278 Z= 0.341 Chirality : 0.047 0.425 2190 Planarity : 0.004 0.056 2598 Dihedral : 5.364 30.889 1974 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.07 % Favored : 86.38 % Rotamer: Outliers : 2.62 % Allowed : 23.08 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -2.25 (0.19), residues: 1806 helix: 0.31 (0.19), residues: 696 sheet: -1.28 (0.55), residues: 108 loop : -3.03 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.022 0.001 TYR A 66 PHE 0.018 0.001 PHE A 344 TRP 0.030 0.001 TRP A 291 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00295 (14980) covalent geometry : angle 0.68375 (20278) hydrogen bonds : bond 0.03027 ( 465) hydrogen bonds : angle 4.48866 ( 1368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8612 (m-30) cc_final: 0.8328 (t0) REVERT: A 397 GLU cc_start: 0.8475 (pm20) cc_final: 0.8097 (pm20) REVERT: A 481 HIS cc_start: 0.8421 (p-80) cc_final: 0.8086 (p-80) REVERT: A 653 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9015 (tp) REVERT: A 702 TYR cc_start: 0.8332 (t80) cc_final: 0.8010 (t80) REVERT: A 860 ASP cc_start: 0.8297 (m-30) cc_final: 0.8051 (m-30) REVERT: A 862 LYS cc_start: 0.8514 (pptt) cc_final: 0.8190 (ptmt) REVERT: B 30 LEU cc_start: 0.9143 (tp) cc_final: 0.8847 (tp) REVERT: B 259 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8188 (p) REVERT: B 397 GLU cc_start: 0.8504 (pm20) cc_final: 0.8101 (pm20) REVERT: B 402 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: B 702 TYR cc_start: 0.8334 (t80) cc_final: 0.8056 (t80) REVERT: B 862 LYS cc_start: 0.8644 (pptt) cc_final: 0.8414 (ptmt) outliers start: 41 outliers final: 28 residues processed: 211 average time/residue: 0.0983 time to fit residues: 33.8290 Evaluate side-chains 195 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain D residue 21 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 11 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.123759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.093751 restraints weight = 36956.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097010 restraints weight = 20318.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099106 restraints weight = 14293.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100404 restraints weight = 11568.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101212 restraints weight = 10178.359| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14980 Z= 0.153 Angle : 0.698 11.057 20278 Z= 0.351 Chirality : 0.048 0.395 2190 Planarity : 0.004 0.056 2598 Dihedral : 5.355 29.819 1974 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.46 % Favored : 85.99 % Rotamer: Outliers : 2.43 % Allowed : 23.79 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.19), residues: 1806 helix: 0.36 (0.19), residues: 696 sheet: -1.29 (0.55), residues: 108 loop : -3.01 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.024 0.001 TYR B 66 PHE 0.019 0.001 PHE A 344 TRP 0.025 0.002 TRP A 291 HIS 0.006 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00357 (14980) covalent geometry : angle 0.69800 (20278) hydrogen bonds : bond 0.03094 ( 465) hydrogen bonds : angle 4.49166 ( 1368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8530 (pm20) cc_final: 0.8155 (pm20) REVERT: A 417 MET cc_start: 0.8582 (tpp) cc_final: 0.7884 (tpp) REVERT: A 481 HIS cc_start: 0.8388 (p-80) cc_final: 0.8065 (p-80) REVERT: A 555 PHE cc_start: 0.6248 (t80) cc_final: 0.5550 (t80) REVERT: A 653 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9029 (tp) REVERT: A 702 TYR cc_start: 0.8372 (t80) cc_final: 0.7977 (t80) REVERT: A 814 LYS cc_start: 0.9292 (tppt) cc_final: 0.8869 (ptpt) REVERT: A 862 LYS cc_start: 0.8479 (pptt) cc_final: 0.8159 (ptmt) REVERT: B 30 LEU cc_start: 0.9182 (tp) cc_final: 0.8890 (tp) REVERT: B 259 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 397 GLU cc_start: 0.8535 (pm20) cc_final: 0.8125 (pm20) REVERT: B 402 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: B 702 TYR cc_start: 0.8365 (t80) cc_final: 0.8039 (t80) REVERT: B 827 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6973 (mp0) outliers start: 38 outliers final: 29 residues processed: 198 average time/residue: 0.0975 time to fit residues: 31.7777 Evaluate side-chains 200 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain D residue 21 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 32 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 ASN ** 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 = 0.3933 r_free = 0.3933 target = 0.124195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.095010 restraints weight = 35913.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098269 restraints weight = 19072.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100385 restraints weight = 13115.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101717 restraints weight = 10483.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.102531 restraints weight = 9163.998| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14980 Z= 0.138 Angle : 0.693 11.364 20278 Z= 0.349 Chirality : 0.047 0.377 2190 Planarity : 0.004 0.056 2598 Dihedral : 5.313 30.703 1974 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.29 % Favored : 86.10 % Rotamer: Outliers : 2.43 % Allowed : 23.98 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -2.17 (0.19), residues: 1806 helix: 0.38 (0.19), residues: 696 sheet: -1.27 (0.55), residues: 108 loop : -2.98 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.024 0.001 TYR B 66 PHE 0.019 0.001 PHE B 503 TRP 0.021 0.002 TRP A 291 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00323 (14980) covalent geometry : angle 0.69311 (20278) hydrogen bonds : bond 0.03047 ( 465) hydrogen bonds : angle 4.45406 ( 1368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8507 (pm20) cc_final: 0.8113 (pm20) REVERT: A 417 MET cc_start: 0.8586 (tpp) cc_final: 0.7876 (tpp) REVERT: A 481 HIS cc_start: 0.8273 (p-80) cc_final: 0.7929 (p-80) REVERT: A 653 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9001 (tp) REVERT: A 702 TYR cc_start: 0.8337 (t80) cc_final: 0.7975 (t80) REVERT: A 862 LYS cc_start: 0.8474 (pptt) cc_final: 0.8188 (ptmt) REVERT: B 30 LEU cc_start: 0.9157 (tp) cc_final: 0.8866 (tp) REVERT: B 259 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 397 GLU cc_start: 0.8535 (pm20) cc_final: 0.8115 (pm20) REVERT: B 402 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: B 595 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.6489 (t80) REVERT: B 702 TYR cc_start: 0.8392 (t80) cc_final: 0.8090 (t80) REVERT: B 820 TYR cc_start: 0.9380 (OUTLIER) cc_final: 0.9122 (m-80) REVERT: B 827 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7283 (mp0) outliers start: 38 outliers final: 30 residues processed: 200 average time/residue: 0.0977 time to fit residues: 32.0718 Evaluate side-chains 200 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 836 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 595 PHE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain D residue 21 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.124398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.095123 restraints weight = 35997.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098401 restraints weight = 19183.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100496 restraints weight = 13238.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101832 restraints weight = 10602.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.102644 restraints weight = 9263.290| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 14980 Z= 0.170 Angle : 0.872 59.199 20278 Z= 0.484 Chirality : 0.050 0.839 2190 Planarity : 0.004 0.056 2598 Dihedral : 5.318 30.498 1974 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.18 % Favored : 86.21 % Rotamer: Outliers : 2.62 % Allowed : 23.91 % Favored : 73.47 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -2.17 (0.19), residues: 1806 helix: 0.38 (0.19), residues: 696 sheet: -1.26 (0.55), residues: 108 loop : -2.98 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 235 TYR 0.022 0.001 TYR B 66 PHE 0.019 0.001 PHE A 344 TRP 0.020 0.002 TRP A 291 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00363 (14980) covalent geometry : angle 0.87249 (20278) hydrogen bonds : bond 0.03047 ( 465) hydrogen bonds : angle 4.45238 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.77 seconds wall clock time: 41 minutes 8.08 seconds (2468.08 seconds total)