Starting phenix.real_space_refine on Sun Oct 13 09:58:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7l_37340/10_2024/8w7l_37340.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7l_37340/10_2024/8w7l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7l_37340/10_2024/8w7l_37340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7l_37340/10_2024/8w7l_37340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7l_37340/10_2024/8w7l_37340.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7l_37340/10_2024/8w7l_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 9.29, per 1000 atoms: 0.63 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: 3.46 Conformation dependent library (CDL) restraints added in 1.9 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: 1.56 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: 4.47 Time building geometry restraints manager: 4.01 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: 8.490 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.600 Find NCS groups from input model: 0.450 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: 0.000 Load rotamer database and sin/cos tables:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.030 ------------------------------------------------------------------------------- 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= 0.348 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 1.810 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: 0.2786 time to fit residues: 119.4876 Evaluate side-chains 179 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.277 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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= 0.391 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 *********************** 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 fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 PHE cc_start: 0.8681 (m-80) cc_final: 0.8439 (m-80) REVERT: A 402 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: A 559 TYR cc_start: 0.8100 (m-10) cc_final: 0.7894 (m-10) REVERT: A 862 LYS cc_start: 0.8777 (pptt) cc_final: 0.8334 (ptmt) REVERT: B 33 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8103 (t0) REVERT: B 183 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6126 (t70) REVERT: B 217 PHE cc_start: 0.8695 (m-80) cc_final: 0.8455 (m-80) REVERT: B 402 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: B 544 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: B 702 TYR cc_start: 0.8031 (t80) cc_final: 0.7718 (t80) REVERT: B 804 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7733 (m-30) outliers start: 32 outliers final: 21 residues processed: 217 average time/residue: 0.2915 time to fit residues: 95.2492 Evaluate side-chains 187 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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 90 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 176 optimal weight: 0.1980 chunk 145 optimal weight: 0.8980 chunk 162 optimal weight: 0.0470 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 432 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14980 Z= 0.164 Angle : 0.637 8.670 20278 Z= 0.326 Chirality : 0.043 0.207 2190 Planarity : 0.004 0.051 2598 Dihedral : 5.605 28.389 1974 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.57 % Favored : 87.82 % Rotamer: Outliers : 1.73 % Allowed : 17.71 % Favored : 80.56 % 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: -2.65 (0.19), residues: 1806 helix: -0.12 (0.19), residues: 688 sheet: -1.35 (0.55), residues: 108 loop : -3.19 (0.17), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 34 HIS 0.003 0.001 HIS A 35 PHE 0.020 0.001 PHE B 344 TYR 0.022 0.001 TYR B 66 ARG 0.003 0.000 ARG A 448 *********************** 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 238 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 211 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 TRP cc_start: 0.8702 (t60) cc_final: 0.8456 (t60) REVERT: A 397 GLU cc_start: 0.8306 (pm20) cc_final: 0.7973 (pm20) REVERT: A 481 HIS cc_start: 0.8419 (p-80) cc_final: 0.8177 (p-80) REVERT: A 814 LYS cc_start: 0.9181 (tppt) cc_final: 0.8896 (ptpt) REVERT: A 862 LYS cc_start: 0.8625 (pptt) cc_final: 0.8263 (ptmt) REVERT: B 30 LEU cc_start: 0.9119 (tp) cc_final: 0.8802 (tp) REVERT: B 79 ILE cc_start: 0.8943 (mm) cc_final: 0.8705 (tp) REVERT: B 217 PHE cc_start: 0.8510 (m-80) cc_final: 0.8185 (m-80) REVERT: B 397 GLU cc_start: 0.8271 (pm20) cc_final: 0.7921 (pm20) REVERT: B 702 TYR cc_start: 0.8106 (t80) cc_final: 0.7820 (t80) REVERT: B 747 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7476 (t) REVERT: B 814 LYS cc_start: 0.9081 (tppt) cc_final: 0.8752 (ptpt) REVERT: B 862 LYS cc_start: 0.8586 (pptt) cc_final: 0.8202 (ptmt) outliers start: 27 outliers final: 10 residues processed: 225 average time/residue: 0.2781 time to fit residues: 95.2284 Evaluate side-chains 182 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 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 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 161 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 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 233 ASN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 14980 Z= 0.400 Angle : 0.742 9.808 20278 Z= 0.387 Chirality : 0.048 0.188 2190 Planarity : 0.005 0.060 2598 Dihedral : 5.915 31.989 1974 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.40 % Favored : 85.99 % Rotamer: Outliers : 2.88 % Allowed : 19.76 % Favored : 77.37 % 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: -2.63 (0.19), residues: 1806 helix: -0.10 (0.19), residues: 694 sheet: -1.75 (0.50), residues: 108 loop : -3.13 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 34 HIS 0.011 0.002 HIS A 81 PHE 0.022 0.002 PHE A 344 TYR 0.026 0.002 TYR A 116 ARG 0.005 0.001 ARG B 155 *********************** 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 218 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8711 (tp) REVERT: A 397 GLU cc_start: 0.8504 (pm20) cc_final: 0.8125 (pm20) REVERT: A 402 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: A 653 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9046 (tp) REVERT: A 702 TYR cc_start: 0.8290 (t80) cc_final: 0.7963 (t80) REVERT: A 747 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7634 (t) REVERT: A 862 LYS cc_start: 0.8534 (pptt) cc_final: 0.8157 (ptmt) REVERT: C 17 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: B 30 LEU cc_start: 0.9235 (tp) cc_final: 0.8936 (tp) REVERT: B 217 PHE cc_start: 0.8621 (m-80) cc_final: 0.8392 (m-80) REVERT: B 259 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 397 GLU cc_start: 0.8526 (pm20) cc_final: 0.8140 (pm20) REVERT: B 402 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: B 702 TYR cc_start: 0.8208 (t80) cc_final: 0.7745 (t80) REVERT: B 747 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7568 (t) REVERT: B 862 LYS cc_start: 0.8550 (pptt) cc_final: 0.8129 (ptmt) outliers start: 45 outliers final: 24 residues processed: 202 average time/residue: 0.2724 time to fit residues: 88.8136 Evaluate side-chains 183 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 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 480 MET Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 694 VAL 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 144 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14980 Z= 0.200 Angle : 0.654 9.926 20278 Z= 0.331 Chirality : 0.045 0.325 2190 Planarity : 0.004 0.057 2598 Dihedral : 5.562 30.631 1974 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.35 % Favored : 87.10 % Rotamer: Outliers : 2.88 % Allowed : 21.04 % Favored : 76.09 % 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: -2.45 (0.19), residues: 1806 helix: 0.06 (0.19), residues: 696 sheet: -1.43 (0.52), residues: 108 loop : -3.07 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 34 HIS 0.005 0.001 HIS A 81 PHE 0.021 0.001 PHE B 344 TYR 0.021 0.001 TYR A 232 ARG 0.003 0.000 ARG A 235 *********************** 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 236 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 191 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 TRP cc_start: 0.8759 (t60) cc_final: 0.8471 (t60) REVERT: A 339 ASP cc_start: 0.8658 (m-30) cc_final: 0.8414 (t0) REVERT: A 397 GLU cc_start: 0.8421 (pm20) cc_final: 0.8061 (pm20) REVERT: A 402 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: A 481 HIS cc_start: 0.8410 (p-80) cc_final: 0.8200 (p-80) REVERT: A 653 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9061 (tp) REVERT: A 747 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7565 (t) REVERT: A 814 LYS cc_start: 0.9287 (tppt) cc_final: 0.8950 (ptpt) REVERT: A 862 LYS cc_start: 0.8419 (pptt) cc_final: 0.8098 (ptmt) REVERT: B 30 LEU cc_start: 0.9146 (tp) cc_final: 0.8855 (tp) REVERT: B 259 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 339 ASP cc_start: 0.8745 (m-30) cc_final: 0.8470 (t0) REVERT: B 397 GLU cc_start: 0.8416 (pm20) cc_final: 0.8051 (pm20) REVERT: B 402 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: B 702 TYR cc_start: 0.8280 (t80) cc_final: 0.7964 (t80) REVERT: B 747 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7551 (t) REVERT: B 862 LYS cc_start: 0.8451 (pptt) cc_final: 0.8109 (ptmt) outliers start: 45 outliers final: 17 residues processed: 223 average time/residue: 0.2692 time to fit residues: 95.4420 Evaluate side-chains 193 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 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 A residue 653 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 108 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 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 0.0270 overall best weight: 2.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14980 Z= 0.273 Angle : 0.681 10.336 20278 Z= 0.348 Chirality : 0.046 0.296 2190 Planarity : 0.004 0.059 2598 Dihedral : 5.588 30.607 1974 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.57 % Favored : 85.88 % Rotamer: Outliers : 3.45 % Allowed : 21.74 % Favored : 74.81 % 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: 0.13 (0.19), residues: 694 sheet: -1.44 (0.52), residues: 108 loop : -3.04 (0.18), 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 0.021 0.001 PHE B 344 TYR 0.024 0.002 TYR B 66 ARG 0.004 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 184 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8673 (m-30) cc_final: 0.8386 (t0) REVERT: A 360 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8661 (tp) REVERT: A 397 GLU cc_start: 0.8448 (pm20) cc_final: 0.8088 (pm20) REVERT: A 402 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8242 (pm20) REVERT: A 439 LYS cc_start: 0.9147 (mttt) cc_final: 0.8881 (mttt) REVERT: A 481 HIS cc_start: 0.8338 (p-80) cc_final: 0.8019 (p-80) REVERT: A 653 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9044 (tp) REVERT: A 702 TYR cc_start: 0.8360 (t80) cc_final: 0.8000 (t80) REVERT: A 747 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7611 (t) REVERT: A 862 LYS cc_start: 0.8572 (pptt) cc_final: 0.8283 (ptmt) REVERT: C 17 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: B 30 LEU cc_start: 0.9190 (tp) cc_final: 0.8902 (tp) REVERT: B 259 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8243 (p) REVERT: B 397 GLU cc_start: 0.8459 (pm20) cc_final: 0.8105 (pm20) REVERT: B 402 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: B 702 TYR cc_start: 0.8335 (t80) cc_final: 0.8006 (t80) REVERT: B 747 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7422 (t) REVERT: B 862 LYS cc_start: 0.8535 (pptt) cc_final: 0.8157 (ptmt) outliers start: 54 outliers final: 29 residues processed: 224 average time/residue: 0.2507 time to fit residues: 89.0910 Evaluate side-chains 203 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 2.178 ------------------------------------------------------------------------------- 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 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 340 LEU Chi-restraints excluded: chain A residue 354 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 653 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain C residue 17 GLU 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 259 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 354 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 534 PHE Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 21 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 358 ASN B 836 ASN ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14980 Z= 0.187 Angle : 0.666 11.630 20278 Z= 0.333 Chirality : 0.046 0.362 2190 Planarity : 0.004 0.056 2598 Dihedral : 5.398 30.395 1974 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.74 % Favored : 86.71 % Rotamer: Outliers : 2.88 % Allowed : 23.08 % Favored : 74.04 % 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: -2.26 (0.19), residues: 1806 helix: 0.22 (0.19), residues: 694 sheet: -1.27 (0.53), residues: 108 loop : -2.96 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 291 HIS 0.005 0.001 HIS A 35 PHE 0.019 0.001 PHE B 344 TYR 0.020 0.001 TYR B 66 ARG 0.003 0.000 ARG A 235 *********************** 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 235 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 190 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8651 (m-30) cc_final: 0.8358 (t0) REVERT: A 397 GLU cc_start: 0.8419 (pm20) cc_final: 0.8070 (pm20) REVERT: A 402 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: A 439 LYS cc_start: 0.9122 (mttt) cc_final: 0.8905 (mttt) REVERT: A 481 HIS cc_start: 0.8195 (p-80) cc_final: 0.7868 (p-80) REVERT: A 555 PHE cc_start: 0.6380 (t80) cc_final: 0.5641 (t80) REVERT: A 653 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9038 (tp) REVERT: A 702 TYR cc_start: 0.8350 (t80) cc_final: 0.8032 (t80) REVERT: A 747 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7465 (t) REVERT: A 814 LYS cc_start: 0.9316 (tppt) cc_final: 0.8964 (ptpt) REVERT: A 862 LYS cc_start: 0.8696 (pptt) cc_final: 0.8444 (ptmt) REVERT: B 30 LEU cc_start: 0.9133 (tp) cc_final: 0.8842 (tp) REVERT: B 259 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 397 GLU cc_start: 0.8425 (pm20) cc_final: 0.8051 (pm20) REVERT: B 402 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8176 (pm20) REVERT: B 702 TYR cc_start: 0.8350 (t80) cc_final: 0.8066 (t80) REVERT: B 747 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7435 (t) REVERT: B 804 ASP cc_start: 0.8095 (m-30) cc_final: 0.7876 (m-30) REVERT: B 862 LYS cc_start: 0.8504 (pptt) cc_final: 0.8132 (ptmt) outliers start: 45 outliers final: 25 residues processed: 220 average time/residue: 0.2485 time to fit residues: 87.8138 Evaluate side-chains 207 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 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 367 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 196 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 545 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 774 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 107 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 GLN ** 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 345 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 14980 Z= 0.434 Angle : 0.796 10.898 20278 Z= 0.407 Chirality : 0.050 0.326 2190 Planarity : 0.005 0.062 2598 Dihedral : 5.955 31.264 1974 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.40 % Favored : 85.05 % Rotamer: Outliers : 3.52 % Allowed : 23.15 % Favored : 73.34 % 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: -2.57 (0.19), residues: 1806 helix: -0.02 (0.19), residues: 706 sheet: -1.93 (0.49), residues: 118 loop : -3.13 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 291 HIS 0.011 0.002 HIS B 89 PHE 0.022 0.002 PHE B 344 TYR 0.028 0.002 TYR A 116 ARG 0.005 0.001 ARG B 155 *********************** 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 224 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 169 time to evaluate : 1.948 Fit side-chains revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8705 (m-30) cc_final: 0.8403 (t0) REVERT: A 397 GLU cc_start: 0.8529 (pm20) cc_final: 0.8169 (pm20) REVERT: A 417 MET cc_start: 0.8698 (tpp) cc_final: 0.8071 (tpp) REVERT: A 653 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9013 (tp) REVERT: A 702 TYR cc_start: 0.8413 (t80) cc_final: 0.7798 (t80) REVERT: A 747 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7608 (t) REVERT: C 17 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: B 30 LEU cc_start: 0.9241 (tp) cc_final: 0.8960 (tp) REVERT: B 259 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 397 GLU cc_start: 0.8504 (pm20) cc_final: 0.8150 (pm20) REVERT: B 595 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6857 (t80) REVERT: B 702 TYR cc_start: 0.8442 (t80) cc_final: 0.7978 (t80) REVERT: B 862 LYS cc_start: 0.8652 (pptt) cc_final: 0.8214 (ptmt) outliers start: 55 outliers final: 36 residues processed: 209 average time/residue: 0.2552 time to fit residues: 86.0861 Evaluate side-chains 196 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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 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 196 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain C residue 17 GLU 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 181 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 595 PHE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 774 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 157 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 161 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14980 Z= 0.285 Angle : 0.741 10.693 20278 Z= 0.375 Chirality : 0.048 0.356 2190 Planarity : 0.004 0.058 2598 Dihedral : 5.743 32.567 1974 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.12 % Favored : 86.32 % Rotamer: Outliers : 2.75 % Allowed : 24.10 % Favored : 73.15 % 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: -2.45 (0.19), residues: 1806 helix: 0.12 (0.19), residues: 696 sheet: -1.66 (0.52), residues: 108 loop : -3.08 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 291 HIS 0.008 0.001 HIS A 35 PHE 0.021 0.001 PHE B 344 TYR 0.023 0.001 TYR A 232 ARG 0.004 0.000 ARG A 235 *********************** 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 210 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8668 (m-30) cc_final: 0.8417 (t0) REVERT: A 397 GLU cc_start: 0.8448 (pm20) cc_final: 0.8056 (pm20) REVERT: A 439 LYS cc_start: 0.9169 (mttt) cc_final: 0.8901 (ttmm) REVERT: A 653 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9022 (tp) REVERT: A 702 TYR cc_start: 0.8397 (t80) cc_final: 0.7801 (t80) REVERT: A 747 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7442 (t) REVERT: C 17 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: B 12 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: B 30 LEU cc_start: 0.9211 (tp) cc_final: 0.8913 (tp) REVERT: B 238 GLU cc_start: 0.8396 (mp0) cc_final: 0.7590 (tm-30) REVERT: B 259 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8259 (p) REVERT: B 397 GLU cc_start: 0.8454 (pm20) cc_final: 0.8060 (pm20) REVERT: B 595 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6822 (t80) REVERT: B 702 TYR cc_start: 0.8448 (t80) cc_final: 0.8039 (t80) REVERT: B 862 LYS cc_start: 0.8640 (pptt) cc_final: 0.8238 (ptmt) outliers start: 43 outliers final: 32 residues processed: 198 average time/residue: 0.1835 time to fit residues: 59.5638 Evaluate side-chains 201 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain C residue 17 GLU 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 181 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 595 PHE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 774 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 170 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 165 optimal weight: 0.0870 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14980 Z= 0.228 Angle : 0.718 11.606 20278 Z= 0.361 Chirality : 0.048 0.523 2190 Planarity : 0.004 0.057 2598 Dihedral : 5.569 30.461 1974 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.29 % Favored : 86.16 % Rotamer: Outliers : 2.69 % Allowed : 24.49 % Favored : 72.83 % 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: -2.31 (0.19), residues: 1806 helix: 0.24 (0.19), residues: 696 sheet: -1.47 (0.53), residues: 108 loop : -3.03 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 291 HIS 0.007 0.001 HIS A 35 PHE 0.020 0.001 PHE B 344 TYR 0.021 0.001 TYR A 232 ARG 0.005 0.000 ARG A 654 ********************** 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 222 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8657 (m-30) cc_final: 0.8417 (t0) REVERT: A 397 GLU cc_start: 0.8439 (pm20) cc_final: 0.8095 (pm20) REVERT: A 439 LYS cc_start: 0.9137 (mttt) cc_final: 0.8911 (ttmm) REVERT: A 481 HIS cc_start: 0.8297 (p-80) cc_final: 0.8045 (p-80) REVERT: A 555 PHE cc_start: 0.6420 (t80) cc_final: 0.5805 (t80) REVERT: A 653 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9010 (tp) REVERT: A 702 TYR cc_start: 0.8501 (t80) cc_final: 0.7963 (t80) REVERT: B 12 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: B 30 LEU cc_start: 0.9167 (tp) cc_final: 0.8876 (tp) REVERT: B 259 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 397 GLU cc_start: 0.8446 (pm20) cc_final: 0.8045 (pm20) REVERT: B 595 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6708 (t80) REVERT: B 702 TYR cc_start: 0.8451 (t80) cc_final: 0.8074 (t80) REVERT: B 827 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: B 862 LYS cc_start: 0.8582 (pptt) cc_final: 0.8230 (ptmt) outliers start: 42 outliers final: 31 residues processed: 206 average time/residue: 0.2417 time to fit residues: 79.7642 Evaluate side-chains 201 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 595 PHE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain D residue 21 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: