Starting phenix.real_space_refine on Fri Jun 13 04:00:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w7l_37340/06_2025/8w7l_37340.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w7l_37340/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w7l_37340/06_2025/8w7l_37340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w7l_37340/06_2025/8w7l_37340.map" model { file = "/net/cci-nas-00/data/ceres_data/8w7l_37340/06_2025/8w7l_37340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w7l_37340/06_2025/8w7l_37340.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2, '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: {'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2, '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: 8.48, per 1000 atoms: 0.58 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.44 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: 4.62 Time building geometry restraints manager: 4.02 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: 0.00 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: 1.210 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 34.300 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.002 TRP A 43 HIS 0.011 0.001 HIS A 413 PHE 0.058 0.002 PHE B 503 TYR 0.035 0.002 TYR A 558 ARG 0.005 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.15879 ( 465) hydrogen bonds : angle 7.41828 ( 1368) covalent geometry : bond 0.00523 (14980) covalent geometry : angle 1.15413 (20278) *********************** 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 : 1.553 Fit side-chains 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: 0.8426 (tp) REVERT: A 199 ASP cc_start: 0.7379 (p0) cc_final: 0.7162 (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: 0.7940 (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: 0.8552 (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: 0.7945 (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: 0.8018 (tmtt) REVERT: B 864 THR cc_start: 0.8433 (p) cc_final: 0.8192 (p) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.2398 time to fit residues: 102.8331 Evaluate side-chains 179 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 GLN B 731 ASN ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.123102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.093809 restraints weight = 35859.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097000 restraints weight = 19463.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.099058 restraints weight = 13502.388| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2764 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= 0.268 Angle : 0.777 10.097 20278 Z= 0.410 Chirality : 0.048 0.251 2190 Planarity : 0.005 0.057 2598 Dihedral : 6.143 33.190 1974 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.66 % Allowed : 12.79 % Favored : 86.54 % Rotamer: Outliers : 2.05 % Allowed : 13.36 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.18), residues: 1806 helix: -0.59 (0.19), residues: 690 sheet: -1.60 (0.57), residues: 104 loop : -3.30 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 43 HIS 0.011 0.002 HIS A 81 PHE 0.024 0.002 PHE B 344 TYR 0.031 0.002 TYR B 232 ARG 0.005 0.001 ARG A 224 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 465) hydrogen bonds : angle 5.29042 ( 1368) covalent geometry : bond 0.00604 (14980) covalent geometry : angle 0.77726 (20278) *********************** 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 231 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 PHE cc_start: 0.8724 (m-80) cc_final: 0.8501 (m-80) REVERT: A 402 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: A 559 TYR cc_start: 0.8291 (m-10) cc_final: 0.8070 (m-10) REVERT: A 862 LYS cc_start: 0.8774 (pptt) cc_final: 0.8319 (ptmt) REVERT: B 33 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8073 (t0) REVERT: B 183 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6124 (t70) REVERT: B 217 PHE cc_start: 0.8719 (m-80) cc_final: 0.8491 (m-80) REVERT: B 402 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: B 544 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: B 702 TYR cc_start: 0.8040 (t80) cc_final: 0.7720 (t80) REVERT: B 804 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7779 (m-30) outliers start: 32 outliers final: 21 residues processed: 217 average time/residue: 0.2501 time to fit residues: 83.0568 Evaluate side-chains 187 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 63 SER 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 49 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 183 ASP 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 582 PHE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 804 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 38 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 0.0670 chunk 31 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 432 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 HIS B 432 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.129189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099993 restraints weight = 35577.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.103426 restraints weight = 19042.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105648 restraints weight = 13038.680| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14980 Z= 0.111 Angle : 0.633 8.582 20278 Z= 0.324 Chirality : 0.043 0.209 2190 Planarity : 0.004 0.050 2598 Dihedral : 5.550 28.416 1974 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.57 % Favored : 87.82 % Rotamer: Outliers : 1.66 % Allowed : 17.71 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.19), residues: 1806 helix: -0.08 (0.19), residues: 688 sheet: -1.34 (0.55), residues: 108 loop : -3.18 (0.17), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 34 HIS 0.003 0.000 HIS A 35 PHE 0.020 0.001 PHE B 344 TYR 0.023 0.001 TYR B 66 ARG 0.002 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 465) hydrogen bonds : angle 4.73311 ( 1368) covalent geometry : bond 0.00244 (14980) covalent geometry : angle 0.63273 (20278) *********************** 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 241 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8587 (tp) cc_final: 0.8010 (tt) REVERT: A 291 TRP cc_start: 0.8727 (t60) cc_final: 0.8483 (t60) REVERT: A 397 GLU cc_start: 0.8319 (pm20) cc_final: 0.7958 (pm20) REVERT: A 481 HIS cc_start: 0.8509 (p-80) cc_final: 0.8271 (p-80) REVERT: A 559 TYR cc_start: 0.8226 (m-10) cc_final: 0.8005 (m-10) REVERT: A 814 LYS cc_start: 0.9194 (tppt) cc_final: 0.8911 (pttm) REVERT: A 862 LYS cc_start: 0.8585 (pptt) cc_final: 0.8221 (ptmt) REVERT: B 30 LEU cc_start: 0.9110 (tp) cc_final: 0.8766 (tp) REVERT: B 79 ILE cc_start: 0.8965 (mm) cc_final: 0.8708 (tp) REVERT: B 217 PHE cc_start: 0.8514 (m-80) cc_final: 0.8306 (m-80) REVERT: B 397 GLU cc_start: 0.8346 (pm20) cc_final: 0.7981 (pm20) REVERT: B 544 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: B 702 TYR cc_start: 0.8120 (t80) cc_final: 0.7780 (t80) REVERT: B 747 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7419 (t) REVERT: B 814 LYS cc_start: 0.9079 (tppt) cc_final: 0.8876 (pttm) REVERT: B 862 LYS cc_start: 0.8649 (pptt) cc_final: 0.8286 (ptmt) outliers start: 26 outliers final: 11 residues processed: 228 average time/residue: 0.2494 time to fit residues: 88.0789 Evaluate side-chains 181 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 633 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 23 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 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 233 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 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 = 0.3931 r_free = 0.3931 target = 0.124026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094508 restraints weight = 35892.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097721 restraints weight = 19656.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.099806 restraints weight = 13722.105| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14980 Z= 0.188 Angle : 0.670 9.611 20278 Z= 0.346 Chirality : 0.046 0.355 2190 Planarity : 0.004 0.056 2598 Dihedral : 5.580 31.012 1974 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.46 % Favored : 86.93 % Rotamer: Outliers : 2.11 % Allowed : 20.14 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.19), residues: 1806 helix: 0.06 (0.19), residues: 694 sheet: -1.55 (0.52), residues: 108 loop : -3.14 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 34 HIS 0.008 0.001 HIS A 81 PHE 0.020 0.001 PHE A 344 TYR 0.022 0.002 TYR A 232 ARG 0.003 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 465) hydrogen bonds : angle 4.76657 ( 1368) covalent geometry : bond 0.00432 (14980) covalent geometry : angle 0.66965 (20278) *********************** 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 216 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8460 (pm20) cc_final: 0.8107 (pm20) REVERT: A 402 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: A 481 HIS cc_start: 0.8619 (p-80) cc_final: 0.8382 (p-80) REVERT: A 862 LYS cc_start: 0.8592 (pptt) cc_final: 0.8231 (ptmt) REVERT: B 30 LEU cc_start: 0.9191 (tp) cc_final: 0.8890 (tp) REVERT: B 168 LYS cc_start: 0.8224 (mttt) cc_final: 0.7988 (mttt) REVERT: B 259 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 397 GLU cc_start: 0.8512 (pm20) cc_final: 0.8141 (pm20) REVERT: B 402 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: B 544 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: B 702 TYR cc_start: 0.8183 (t80) cc_final: 0.7790 (t80) REVERT: B 747 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7448 (t) REVERT: B 862 LYS cc_start: 0.8538 (pptt) cc_final: 0.8174 (ptmt) outliers start: 33 outliers final: 17 residues processed: 203 average time/residue: 0.2412 time to fit residues: 79.7708 Evaluate side-chains 181 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 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 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain B residue 12 PHE 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 367 ILE 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 544 GLN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 826 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 43 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 164 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 92 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 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 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.127077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097563 restraints weight = 35996.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.100988 restraints weight = 19322.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103190 restraints weight = 13277.600| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3258 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= 0.115 Angle : 0.628 9.981 20278 Z= 0.317 Chirality : 0.044 0.360 2190 Planarity : 0.004 0.054 2598 Dihedral : 5.318 29.027 1974 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.55 % Allowed : 11.85 % Favored : 87.60 % Rotamer: Outliers : 2.37 % Allowed : 21.29 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.19), residues: 1806 helix: 0.21 (0.19), residues: 694 sheet: -1.26 (0.54), residues: 108 loop : -3.06 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 291 HIS 0.004 0.001 HIS A 81 PHE 0.018 0.001 PHE B 344 TYR 0.023 0.001 TYR A 66 ARG 0.003 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.02976 ( 465) hydrogen bonds : angle 4.51313 ( 1368) covalent geometry : bond 0.00264 (14980) covalent geometry : angle 0.62792 (20278) *********************** 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 238 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8602 (tp) REVERT: A 397 GLU cc_start: 0.8403 (pm20) cc_final: 0.8056 (pm20) REVERT: A 402 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: A 481 HIS cc_start: 0.8393 (p-80) cc_final: 0.8084 (p-80) REVERT: A 541 TRP cc_start: 0.8788 (t60) cc_final: 0.8508 (t60) REVERT: A 814 LYS cc_start: 0.9300 (tppt) cc_final: 0.8993 (ptpt) REVERT: A 862 LYS cc_start: 0.8520 (pptt) cc_final: 0.8200 (ptmt) REVERT: B 30 LEU cc_start: 0.9134 (tp) cc_final: 0.8819 (tp) REVERT: B 259 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8135 (p) REVERT: B 397 GLU cc_start: 0.8422 (pm20) cc_final: 0.8070 (pm20) REVERT: B 402 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: B 544 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8038 (mt0) REVERT: B 747 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7524 (t) REVERT: B 814 LYS cc_start: 0.9331 (tppt) cc_final: 0.8990 (ptpt) REVERT: B 862 LYS cc_start: 0.8531 (pptt) cc_final: 0.8201 (ptmt) outliers start: 37 outliers final: 15 residues processed: 224 average time/residue: 0.2186 time to fit residues: 78.5118 Evaluate side-chains 203 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 360 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 B residue 12 PHE 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 367 ILE 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 582 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 145 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 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** C 14 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.122923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.093642 restraints weight = 36163.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096851 restraints weight = 19593.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.098899 restraints weight = 13616.771| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14980 Z= 0.185 Angle : 0.678 8.745 20278 Z= 0.347 Chirality : 0.046 0.238 2190 Planarity : 0.004 0.059 2598 Dihedral : 5.452 29.709 1974 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.74 % Favored : 86.66 % Rotamer: Outliers : 3.01 % Allowed : 22.12 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1806 helix: 0.22 (0.19), residues: 694 sheet: -1.46 (0.53), residues: 108 loop : -3.03 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 291 HIS 0.009 0.001 HIS A 81 PHE 0.019 0.001 PHE B 344 TYR 0.021 0.001 TYR A 232 ARG 0.004 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 465) hydrogen bonds : angle 4.59184 ( 1368) covalent geometry : bond 0.00429 (14980) covalent geometry : angle 0.67797 (20278) *********************** 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 230 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: A 360 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8648 (tp) REVERT: A 397 GLU cc_start: 0.8491 (pm20) cc_final: 0.8106 (pm20) REVERT: A 402 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: A 481 HIS cc_start: 0.8523 (p-80) cc_final: 0.8244 (p-80) REVERT: A 702 TYR cc_start: 0.8273 (t80) cc_final: 0.7960 (t80) REVERT: A 862 LYS cc_start: 0.8504 (pptt) cc_final: 0.8197 (ptmt) REVERT: B 30 LEU cc_start: 0.9195 (tp) cc_final: 0.8909 (tp) REVERT: B 259 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8221 (p) REVERT: B 397 GLU cc_start: 0.8516 (pm20) cc_final: 0.8113 (pm20) REVERT: B 402 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: B 544 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: B 594 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: B 702 TYR cc_start: 0.7927 (t80) cc_final: 0.7611 (t80) REVERT: B 862 LYS cc_start: 0.8607 (pptt) cc_final: 0.8225 (ptmt) outliers start: 47 outliers final: 26 residues processed: 219 average time/residue: 0.2047 time to fit residues: 72.3262 Evaluate side-chains 204 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 83 MET 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 360 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 742 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain B residue 12 PHE 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 181 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 367 ILE 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 550 VAL Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 742 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 144 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.126402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.097426 restraints weight = 35955.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100778 restraints weight = 19148.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102975 restraints weight = 13133.325| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14980 Z= 0.116 Angle : 0.649 9.527 20278 Z= 0.326 Chirality : 0.044 0.205 2190 Planarity : 0.004 0.054 2598 Dihedral : 5.254 29.331 1974 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.57 % Favored : 86.88 % Rotamer: Outliers : 2.94 % Allowed : 21.48 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.19), residues: 1806 helix: 0.25 (0.19), residues: 698 sheet: -1.23 (0.54), residues: 108 loop : -2.97 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 291 HIS 0.007 0.001 HIS B 413 PHE 0.017 0.001 PHE B 344 TYR 0.019 0.001 TYR A 543 ARG 0.003 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 465) hydrogen bonds : angle 4.40995 ( 1368) covalent geometry : bond 0.00265 (14980) covalent geometry : angle 0.64919 (20278) *********************** 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 241 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8156 (m-80) cc_final: 0.7953 (m-80) REVERT: A 360 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8624 (tp) REVERT: A 397 GLU cc_start: 0.8466 (pm20) cc_final: 0.8059 (pm20) REVERT: A 402 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8216 (pm20) REVERT: A 481 HIS cc_start: 0.8395 (p-80) cc_final: 0.8097 (p-80) REVERT: A 702 TYR cc_start: 0.8216 (t80) cc_final: 0.7948 (t80) REVERT: A 814 LYS cc_start: 0.9342 (tppt) cc_final: 0.8975 (ptpt) REVERT: A 862 LYS cc_start: 0.8646 (pptt) cc_final: 0.8340 (ptmt) REVERT: C 16 ASP cc_start: 0.8582 (p0) cc_final: 0.8357 (p0) REVERT: B 30 LEU cc_start: 0.9141 (tp) cc_final: 0.8833 (tp) REVERT: B 268 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: B 397 GLU cc_start: 0.8482 (pm20) cc_final: 0.8068 (pm20) REVERT: B 402 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8220 (pm20) REVERT: B 544 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: B 702 TYR cc_start: 0.8021 (t80) cc_final: 0.7699 (t80) REVERT: B 814 LYS cc_start: 0.9288 (tppt) cc_final: 0.8934 (ptpt) REVERT: B 862 LYS cc_start: 0.8536 (pptt) cc_final: 0.8180 (ptmt) outliers start: 46 outliers final: 26 residues processed: 226 average time/residue: 0.2125 time to fit residues: 78.0336 Evaluate side-chains 210 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 VAL 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 360 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 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 367 ILE 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 550 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 788 LEU 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 88 optimal weight: 8.9990 chunk 117 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** A 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3926 r_free = 0.3926 target = 0.123584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094297 restraints weight = 35856.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097533 restraints weight = 19139.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099638 restraints weight = 13219.727| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14980 Z= 0.165 Angle : 0.691 9.811 20278 Z= 0.347 Chirality : 0.048 0.414 2190 Planarity : 0.004 0.057 2598 Dihedral : 5.333 29.238 1974 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.90 % Favored : 86.54 % Rotamer: Outliers : 2.81 % Allowed : 21.87 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.19), residues: 1806 helix: 0.29 (0.19), residues: 696 sheet: -1.22 (0.54), residues: 108 loop : -2.98 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 291 HIS 0.008 0.001 HIS A 81 PHE 0.018 0.001 PHE B 344 TYR 0.020 0.001 TYR B 232 ARG 0.003 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 465) hydrogen bonds : angle 4.49850 ( 1368) covalent geometry : bond 0.00385 (14980) covalent geometry : angle 0.69088 (20278) *********************** 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 227 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8257 (m-80) cc_final: 0.8018 (m-80) REVERT: A 268 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8050 (tp30) REVERT: A 360 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8636 (tp) REVERT: A 397 GLU cc_start: 0.8481 (pm20) cc_final: 0.8070 (pm20) REVERT: A 402 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: A 439 LYS cc_start: 0.9173 (mttt) cc_final: 0.8927 (mttt) REVERT: A 481 HIS cc_start: 0.8519 (p-80) cc_final: 0.8275 (p-80) REVERT: A 702 TYR cc_start: 0.8262 (t80) cc_final: 0.7880 (t80) REVERT: B 30 LEU cc_start: 0.9191 (tp) cc_final: 0.8900 (tp) REVERT: B 268 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8446 (tp30) REVERT: B 397 GLU cc_start: 0.8515 (pm20) cc_final: 0.8099 (pm20) REVERT: B 402 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: B 439 LYS cc_start: 0.8999 (mttt) cc_final: 0.8757 (mtmt) REVERT: B 544 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: B 594 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: B 702 TYR cc_start: 0.8104 (t80) cc_final: 0.7725 (t80) REVERT: B 862 LYS cc_start: 0.8579 (pptt) cc_final: 0.8197 (ptmt) outliers start: 44 outliers final: 28 residues processed: 213 average time/residue: 0.2149 time to fit residues: 73.8059 Evaluate side-chains 210 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 268 GLU 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 618 ASN Chi-restraints excluded: chain A residue 633 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 87 PHE Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 367 ILE 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 550 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 742 LEU 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 43 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.119661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089888 restraints weight = 36181.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.093032 restraints weight = 19500.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095061 restraints weight = 13573.652| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 14980 Z= 0.240 Angle : 0.761 10.675 20278 Z= 0.386 Chirality : 0.049 0.282 2190 Planarity : 0.004 0.059 2598 Dihedral : 5.721 31.297 1974 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.73 % Favored : 85.71 % Rotamer: Outliers : 2.75 % Allowed : 22.25 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.19), residues: 1806 helix: 0.12 (0.19), residues: 698 sheet: -1.39 (0.54), residues: 108 loop : -3.05 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 34 HIS 0.009 0.002 HIS A 35 PHE 0.021 0.002 PHE B 344 TYR 0.023 0.002 TYR A 232 ARG 0.005 0.001 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 465) hydrogen bonds : angle 4.73393 ( 1368) covalent geometry : bond 0.00556 (14980) covalent geometry : angle 0.76067 (20278) *********************** 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 218 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: A 397 GLU cc_start: 0.8592 (pm20) cc_final: 0.8215 (pm20) REVERT: A 555 PHE cc_start: 0.6490 (t80) cc_final: 0.5816 (t80) REVERT: A 862 LYS cc_start: 0.8748 (pptt) cc_final: 0.8541 (ptmt) REVERT: B 30 LEU cc_start: 0.9227 (tp) cc_final: 0.8933 (tp) REVERT: B 339 ASP cc_start: 0.8706 (m-30) cc_final: 0.8402 (t0) REVERT: B 397 GLU cc_start: 0.8617 (pm20) cc_final: 0.8243 (pm20) REVERT: B 544 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: B 594 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 702 TYR cc_start: 0.8233 (t80) cc_final: 0.7730 (t80) REVERT: B 862 LYS cc_start: 0.8593 (pptt) cc_final: 0.8233 (ptmt) outliers start: 43 outliers final: 28 residues processed: 208 average time/residue: 0.2040 time to fit residues: 69.0209 Evaluate side-chains 196 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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 268 GLU 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 A residue 742 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 826 ILE 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 181 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 788 LEU 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 2 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 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 355 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.124809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095751 restraints weight = 35886.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099058 restraints weight = 19028.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101186 restraints weight = 13079.261| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4053 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= 0.128 Angle : 0.700 11.886 20278 Z= 0.348 Chirality : 0.048 0.493 2190 Planarity : 0.004 0.053 2598 Dihedral : 5.423 30.458 1974 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.40 % Favored : 87.04 % Rotamer: Outliers : 1.98 % Allowed : 23.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.19), residues: 1806 helix: 0.25 (0.19), residues: 698 sheet: -1.01 (0.56), residues: 108 loop : -2.95 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 291 HIS 0.007 0.001 HIS A 35 PHE 0.020 0.001 PHE A 534 TYR 0.018 0.001 TYR B 232 ARG 0.004 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 465) hydrogen bonds : angle 4.49231 ( 1368) covalent geometry : bond 0.00292 (14980) covalent geometry : angle 0.69966 (20278) ********************** 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 212 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: A 291 TRP cc_start: 0.8880 (t60) cc_final: 0.8028 (t60) REVERT: A 417 MET cc_start: 0.8578 (tpp) cc_final: 0.7826 (tpp) REVERT: A 439 LYS cc_start: 0.9172 (mttt) cc_final: 0.8937 (mttt) REVERT: A 481 HIS cc_start: 0.8435 (p-80) cc_final: 0.8180 (p-80) REVERT: A 702 TYR cc_start: 0.8357 (t80) cc_final: 0.7989 (t80) REVERT: B 30 LEU cc_start: 0.9155 (tp) cc_final: 0.8865 (tp) REVERT: B 123 GLU cc_start: 0.7776 (mp0) cc_final: 0.7309 (mp0) REVERT: B 339 ASP cc_start: 0.8674 (m-30) cc_final: 0.8361 (t0) REVERT: B 397 GLU cc_start: 0.8494 (pm20) cc_final: 0.8077 (pm20) REVERT: B 417 MET cc_start: 0.8606 (tpt) cc_final: 0.8218 (tpt) REVERT: B 544 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: B 594 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: B 702 TYR cc_start: 0.8339 (t80) cc_final: 0.7873 (t80) REVERT: B 862 LYS cc_start: 0.8691 (pptt) cc_final: 0.8346 (ptmt) outliers start: 31 outliers final: 22 residues processed: 201 average time/residue: 0.1988 time to fit residues: 65.2233 Evaluate side-chains 198 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 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 633 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 181 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 594 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 788 LEU 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 177 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.122126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.092709 restraints weight = 36143.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095922 restraints weight = 19209.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098016 restraints weight = 13280.169| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14980 Z= 0.177 Angle : 0.722 11.406 20278 Z= 0.363 Chirality : 0.048 0.439 2190 Planarity : 0.004 0.058 2598 Dihedral : 5.462 30.020 1974 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.40 % Favored : 85.99 % Rotamer: Outliers : 1.66 % Allowed : 23.85 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.19), residues: 1806 helix: 0.30 (0.19), residues: 696 sheet: -1.15 (0.56), residues: 108 loop : -2.97 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 541 HIS 0.008 0.001 HIS A 35 PHE 0.024 0.001 PHE B 200 TYR 0.021 0.001 TYR B 232 ARG 0.003 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 465) hydrogen bonds : angle 4.55147 ( 1368) covalent geometry : bond 0.00416 (14980) covalent geometry : angle 0.72159 (20278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4329.34 seconds wall clock time: 76 minutes 37.80 seconds (4597.80 seconds total)