Starting phenix.real_space_refine on Fri Sep 27 19:07:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyf_33520/09_2024/7xyf_33520.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyf_33520/09_2024/7xyf_33520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyf_33520/09_2024/7xyf_33520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyf_33520/09_2024/7xyf_33520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyf_33520/09_2024/7xyf_33520.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xyf_33520/09_2024/7xyf_33520.cif" } resolution = 4.3 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Se 24 7.20 5 P 292 5.49 5 S 25 5.16 5 C 10029 2.51 5 N 3164 2.21 5 O 3787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17321 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 753 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3009 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "I" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2977 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 5281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5281 Classifications: {'peptide': 656} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 631} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 9.51, per 1000 atoms: 0.55 Number of scatterers: 17321 At special positions: 0 Unit cell: (134.16, 140.4, 135.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 24 33.99 S 25 16.00 P 292 15.00 O 3787 8.00 N 3164 7.00 C 10029 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: 4.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 9 sheets defined 61.9% alpha, 3.3% beta 132 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 8.17 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.590A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.632A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 removed outlier: 4.091A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.515A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.590A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.631A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 removed outlier: 4.092A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.515A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.624A pdb=" N ARG B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.980A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.806A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.286A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.663A pdb=" N ARG F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.176A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.745A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.575A pdb=" N ILE C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.101A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.505A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.559A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.627A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.155A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.717A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.682A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.954A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.536A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.869A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.891A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 44 Processing helix chain 'H' and resid 52 through 82 removed outlier: 3.502A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.906A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.805A pdb=" N THR H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 248 removed outlier: 3.626A pdb=" N GLU K 239 " --> pdb=" O ALA K 235 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 242 " --> pdb=" O LYS K 238 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG K 247 " --> pdb=" O LYS K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 258 removed outlier: 3.706A pdb=" N MSE K 256 " --> pdb=" O ASP K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 271 removed outlier: 3.736A pdb=" N LYS K 270 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG K 271 " --> pdb=" O MSE K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 281 Processing helix chain 'K' and resid 301 through 340 removed outlier: 3.743A pdb=" N GLU K 312 " --> pdb=" O GLY K 308 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE K 318 " --> pdb=" O MSE K 314 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN K 326 " --> pdb=" O ALA K 322 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU K 330 " --> pdb=" O GLN K 326 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY K 332 " --> pdb=" O GLU K 328 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS K 333 " --> pdb=" O GLN K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 348 through 352 Processing helix chain 'K' and resid 359 through 366 removed outlier: 3.514A pdb=" N PHE K 365 " --> pdb=" O GLN K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 404 removed outlier: 3.673A pdb=" N ILE K 395 " --> pdb=" O GLN K 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN K 396 " --> pdb=" O ILE K 392 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU K 404 " --> pdb=" O LEU K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 432 Processing helix chain 'K' and resid 443 through 446 Processing helix chain 'K' and resid 447 through 458 removed outlier: 3.822A pdb=" N LEU K 451 " --> pdb=" O MSE K 447 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA K 455 " --> pdb=" O LEU K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 482 Processing helix chain 'K' and resid 493 through 500 removed outlier: 3.515A pdb=" N ALA K 497 " --> pdb=" O THR K 493 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA K 498 " --> pdb=" O TYR K 494 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR K 499 " --> pdb=" O ARG K 495 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER K 500 " --> pdb=" O LEU K 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 493 through 500' Processing helix chain 'K' and resid 500 through 509 Processing helix chain 'K' and resid 521 through 525 Processing helix chain 'K' and resid 528 through 537 removed outlier: 3.768A pdb=" N ARG K 532 " --> pdb=" O SER K 528 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE K 537 " --> pdb=" O HIS K 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 565 removed outlier: 3.836A pdb=" N SER K 559 " --> pdb=" O LYS K 555 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE K 563 " --> pdb=" O SER K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 576 through 581 Processing helix chain 'K' and resid 593 through 607 removed outlier: 3.866A pdb=" N MSE K 606 " --> pdb=" O ARG K 602 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 644 removed outlier: 3.961A pdb=" N ARG K 642 " --> pdb=" O GLU K 638 " (cutoff:3.500A) Processing helix chain 'K' and resid 645 through 648 Processing helix chain 'K' and resid 670 through 675 Processing helix chain 'K' and resid 678 through 689 removed outlier: 4.317A pdb=" N LEU K 682 " --> pdb=" O ALA K 678 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 695 removed outlier: 3.548A pdb=" N PHE K 695 " --> pdb=" O PRO K 692 " (cutoff:3.500A) Processing helix chain 'K' and resid 702 through 710 removed outlier: 3.646A pdb=" N GLN K 706 " --> pdb=" O ASP K 702 " (cutoff:3.500A) Processing helix chain 'K' and resid 724 through 729 Processing helix chain 'K' and resid 733 through 740 Processing helix chain 'K' and resid 760 through 765 removed outlier: 3.571A pdb=" N LYS K 765 " --> pdb=" O THR K 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 765 through 771 Processing helix chain 'K' and resid 786 through 794 Processing helix chain 'K' and resid 864 through 868 removed outlier: 4.000A pdb=" N ASP K 868 " --> pdb=" O GLN K 865 " (cutoff:3.500A) Processing helix chain 'K' and resid 889 through 894 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.707A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.623A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.955A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.759A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 96 through 97 removed outlier: 6.741A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'K' and resid 407 through 410 removed outlier: 6.719A pdb=" N ASN K 513 " --> pdb=" O ALA K 539 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU K 464 " --> pdb=" O LEU K 491 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 627 through 628 removed outlier: 6.595A pdb=" N THR K 627 " --> pdb=" O VAL K 881 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LYS K 883 " --> pdb=" O THR K 627 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL K 851 " --> pdb=" O TYR K 882 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL K 781 " --> pdb=" O ILE K 852 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE K 832 " --> pdb=" O VAL K 780 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU K 782 " --> pdb=" O PHE K 832 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 519 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 318 hydrogen bonds 580 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 8.47 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 5496 1.36 - 1.52: 8388 1.52 - 1.67: 4257 1.67 - 1.83: 37 1.83 - 1.98: 48 Bond restraints: 18226 Sorted by residual: bond pdb=" N LYS K 583 " pdb=" CA LYS K 583 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.79e+00 bond pdb=" N LYS K 574 " pdb=" CA LYS K 574 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.31e-02 5.83e+03 6.57e+00 bond pdb=" N LYS K 753 " pdb=" CA LYS K 753 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.03e+00 bond pdb=" N GLU K 755 " pdb=" CA GLU K 755 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.41e-02 5.03e+03 5.37e+00 bond pdb=" N ASP K 754 " pdb=" CA ASP K 754 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.35e-02 5.49e+03 4.30e+00 ... (remaining 18221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 25042 2.30 - 4.61: 726 4.61 - 6.91: 61 6.91 - 9.21: 9 9.21 - 11.52: 5 Bond angle restraints: 25843 Sorted by residual: angle pdb=" N PHE K 861 " pdb=" CA PHE K 861 " pdb=" C PHE K 861 " ideal model delta sigma weight residual 114.04 108.01 6.03 1.24e+00 6.50e-01 2.36e+01 angle pdb=" N ASP K 754 " pdb=" CA ASP K 754 " pdb=" C ASP K 754 " ideal model delta sigma weight residual 113.23 107.64 5.59 1.22e+00 6.72e-01 2.10e+01 angle pdb=" N LYS K 887 " pdb=" CA LYS K 887 " pdb=" C LYS K 887 " ideal model delta sigma weight residual 110.97 115.90 -4.93 1.09e+00 8.42e-01 2.05e+01 angle pdb=" C VAL K 886 " pdb=" N LYS K 887 " pdb=" CA LYS K 887 " ideal model delta sigma weight residual 120.65 126.52 -5.87 1.32e+00 5.74e-01 1.98e+01 angle pdb=" N ASP K 826 " pdb=" CA ASP K 826 " pdb=" C ASP K 826 " ideal model delta sigma weight residual 110.97 115.79 -4.82 1.09e+00 8.42e-01 1.96e+01 ... (remaining 25838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 8252 30.06 - 60.12: 1934 60.12 - 90.18: 109 90.18 - 120.24: 0 120.24 - 150.31: 3 Dihedral angle restraints: 10298 sinusoidal: 6153 harmonic: 4145 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA K 710 " pdb=" C ALA K 710 " pdb=" N ILE K 711 " pdb=" CA ILE K 711 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA LEU K 737 " pdb=" C LEU K 737 " pdb=" N HIS K 738 " pdb=" CA HIS K 738 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 10295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2154 0.053 - 0.105: 655 0.105 - 0.158: 97 0.158 - 0.210: 17 0.210 - 0.263: 3 Chirality restraints: 2926 Sorted by residual: chirality pdb=" CB ILE K 747 " pdb=" CA ILE K 747 " pdb=" CG1 ILE K 747 " pdb=" CG2 ILE K 747 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB THR K 667 " pdb=" CA THR K 667 " pdb=" OG1 THR K 667 " pdb=" CG2 THR K 667 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE K 309 " pdb=" CA ILE K 309 " pdb=" CG1 ILE K 309 " pdb=" CG2 ILE K 309 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2923 not shown) Planarity restraints: 2271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO G 80 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 714 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO K 715 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO K 715 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 715 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " 0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO F 32 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " 0.038 5.00e-02 4.00e+02 ... (remaining 2268 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3010 2.75 - 3.29: 16314 3.29 - 3.83: 35172 3.83 - 4.36: 40263 4.36 - 4.90: 57843 Nonbonded interactions: 152602 Sorted by model distance: nonbonded pdb=" O LEU E 61 " pdb=" NH2 ARG F 36 " model vdw 2.217 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR K 466 " pdb=" OD1 ASP K 503 " model vdw 2.262 3.040 nonbonded pdb=" O2 DC J 46 " pdb=" N1 DG I 101 " model vdw 2.264 2.496 nonbonded pdb=" OG1 THR A 58 " pdb=" O GLN G 104 " model vdw 2.274 3.040 ... (remaining 152597 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 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } 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=0.46 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: 0.750 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: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 46.190 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.008 0.070 18226 Z= 0.481 Angle : 0.928 11.516 25843 Z= 0.539 Chirality : 0.050 0.263 2926 Planarity : 0.007 0.095 2271 Dihedral : 27.107 150.305 7610 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.14 % Allowed : 10.95 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -4.98 (0.16), residues: 1394 helix: -3.82 (0.10), residues: 783 sheet: -1.65 (0.83), residues: 42 loop : -2.38 (0.21), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP K 757 HIS 0.015 0.002 HIS F 75 PHE 0.028 0.003 PHE K 832 TYR 0.014 0.002 TYR K 731 ARG 0.012 0.001 ARG K 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 342 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8615 (ttm110) cc_final: 0.8190 (mmm-85) REVERT: A 53 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8331 (tpt-90) REVERT: A 61 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8685 (tp) REVERT: A 87 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 129 ARG cc_start: 0.8533 (ttt90) cc_final: 0.8279 (tpp80) REVERT: E 48 LEU cc_start: 0.9139 (tp) cc_final: 0.8635 (tp) REVERT: E 53 ARG cc_start: 0.8514 (ttt180) cc_final: 0.8234 (ttm170) REVERT: E 93 GLN cc_start: 0.8800 (tt0) cc_final: 0.8562 (tt0) REVERT: E 126 LEU cc_start: 0.9480 (tp) cc_final: 0.9073 (tt) REVERT: B 53 GLU cc_start: 0.8302 (tp30) cc_final: 0.7979 (tp30) REVERT: B 79 LYS cc_start: 0.8629 (mttp) cc_final: 0.8200 (mmtm) REVERT: F 62 LEU cc_start: 0.9277 (mp) cc_final: 0.9010 (mp) REVERT: F 88 TYR cc_start: 0.8465 (m-10) cc_final: 0.7982 (m-80) REVERT: C 75 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8271 (mmtm) REVERT: G 36 LYS cc_start: 0.9215 (mttt) cc_final: 0.8929 (mtpp) REVERT: G 38 ASN cc_start: 0.9019 (m110) cc_final: 0.8801 (m110) REVERT: G 79 ILE cc_start: 0.9490 (tp) cc_final: 0.9131 (tp) REVERT: G 91 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7292 (tm-30) REVERT: G 92 GLU cc_start: 0.7617 (tt0) cc_final: 0.7260 (tt0) REVERT: D 43 LYS cc_start: 0.9334 (mmtt) cc_final: 0.8584 (mtpt) REVERT: D 92 GLN cc_start: 0.8734 (tt0) cc_final: 0.8226 (tm-30) REVERT: D 96 ARG cc_start: 0.8423 (mtt180) cc_final: 0.8185 (ttm110) REVERT: H 56 MET cc_start: 0.8449 (tpp) cc_final: 0.8173 (tpp) REVERT: H 102 GLU cc_start: 0.8279 (tp30) cc_final: 0.7872 (tp30) REVERT: K 256 MSE cc_start: 0.4645 (mtt) cc_final: 0.3918 (mtt) REVERT: K 430 MSE cc_start: 0.5807 (ttm) cc_final: 0.5513 (mtp) REVERT: K 535 MSE cc_start: 0.6099 (mmp) cc_final: 0.5601 (mmm) REVERT: K 544 LEU cc_start: 0.6494 (tp) cc_final: 0.6240 (tp) REVERT: K 712 MSE cc_start: -0.1428 (OUTLIER) cc_final: -0.1691 (mmt) REVERT: K 724 TYR cc_start: 0.7215 (m-80) cc_final: 0.6979 (m-10) REVERT: K 731 TYR cc_start: 0.5015 (m-80) cc_final: 0.4743 (m-80) REVERT: K 732 MSE cc_start: -0.0859 (OUTLIER) cc_final: -0.2049 (mmt) REVERT: K 786 PHE cc_start: 0.6131 (t80) cc_final: 0.5885 (t80) REVERT: K 791 ASP cc_start: 0.6706 (m-30) cc_final: 0.6368 (t70) REVERT: K 797 MSE cc_start: 0.2954 (mmm) cc_final: 0.2420 (mmt) REVERT: K 806 ARG cc_start: 0.5690 (ttt180) cc_final: 0.4664 (ttp-110) REVERT: K 851 VAL cc_start: -0.1058 (OUTLIER) cc_final: -0.1947 (p) REVERT: K 872 ARG cc_start: 0.0772 (mmt180) cc_final: -0.0341 (mpt90) outliers start: 26 outliers final: 7 residues processed: 352 average time/residue: 0.4030 time to fit residues: 191.7989 Evaluate side-chains 243 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 231 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 125 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS H 44 GLN H 79 HIS K 335 GLN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 GLN K 706 GLN K 716 GLN K 772 ASN K 812 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18226 Z= 0.245 Angle : 0.692 7.900 25843 Z= 0.399 Chirality : 0.041 0.170 2926 Planarity : 0.006 0.069 2271 Dihedral : 30.578 139.282 4754 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.77 (0.19), residues: 1394 helix: -1.62 (0.15), residues: 812 sheet: -1.66 (0.79), residues: 40 loop : -1.99 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 397 HIS 0.008 0.002 HIS G 31 PHE 0.020 0.002 PHE A 78 TYR 0.041 0.002 TYR H 37 ARG 0.008 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8309 (mmm-85) REVERT: A 53 ARG cc_start: 0.8673 (ttt180) cc_final: 0.8309 (tpt-90) REVERT: A 120 MET cc_start: 0.8610 (mtp) cc_final: 0.8309 (mtp) REVERT: A 126 LEU cc_start: 0.9281 (tp) cc_final: 0.9078 (tp) REVERT: E 48 LEU cc_start: 0.9115 (tp) cc_final: 0.8644 (tp) REVERT: E 53 ARG cc_start: 0.8503 (ttt180) cc_final: 0.8168 (ttm170) REVERT: E 110 CYS cc_start: 0.8779 (m) cc_final: 0.8183 (m) REVERT: E 119 ILE cc_start: 0.9259 (pt) cc_final: 0.9053 (pt) REVERT: E 126 LEU cc_start: 0.9406 (tp) cc_final: 0.9034 (tt) REVERT: B 43 VAL cc_start: 0.9169 (t) cc_final: 0.8940 (p) REVERT: B 79 LYS cc_start: 0.8492 (mttp) cc_final: 0.8219 (mmtm) REVERT: B 84 MET cc_start: 0.7789 (tpp) cc_final: 0.7521 (tpp) REVERT: F 53 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7750 (tm-30) REVERT: F 63 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7992 (mm-30) REVERT: F 88 TYR cc_start: 0.8431 (m-10) cc_final: 0.7716 (m-80) REVERT: G 36 LYS cc_start: 0.9153 (mttt) cc_final: 0.8854 (mtpp) REVERT: G 64 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8622 (tm-30) REVERT: G 91 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7089 (tm-30) REVERT: G 92 GLU cc_start: 0.7803 (tt0) cc_final: 0.7283 (tt0) REVERT: G 102 ILE cc_start: 0.9740 (mm) cc_final: 0.9503 (mm) REVERT: D 36 ILE cc_start: 0.8670 (pt) cc_final: 0.8253 (mp) REVERT: D 43 LYS cc_start: 0.9382 (mmtt) cc_final: 0.8727 (mtpt) REVERT: D 83 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7860 (mtp180) REVERT: D 92 GLN cc_start: 0.8784 (tt0) cc_final: 0.8181 (tm-30) REVERT: D 93 THR cc_start: 0.9308 (m) cc_final: 0.8987 (p) REVERT: D 110 GLU cc_start: 0.8207 (tp30) cc_final: 0.7895 (tm-30) REVERT: H 64 ASN cc_start: 0.9061 (m-40) cc_final: 0.8147 (t0) REVERT: H 102 GLU cc_start: 0.8106 (tp30) cc_final: 0.7403 (tp30) REVERT: K 245 MSE cc_start: 0.0541 (tpt) cc_final: -0.0013 (tpt) REVERT: K 311 MSE cc_start: 0.5232 (mtp) cc_final: 0.3730 (tmm) REVERT: K 535 MSE cc_start: 0.6189 (mmp) cc_final: 0.5661 (mmm) REVERT: K 582 MSE cc_start: 0.4247 (mtm) cc_final: -0.4136 (ttp) REVERT: K 731 TYR cc_start: 0.5263 (m-80) cc_final: 0.4979 (m-80) REVERT: K 769 LEU cc_start: 0.0746 (mt) cc_final: -0.0428 (tp) REVERT: K 786 PHE cc_start: 0.5972 (t80) cc_final: 0.5743 (t80) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3517 time to fit residues: 148.8583 Evaluate side-chains 232 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.0870 chunk 124 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 0.0870 chunk 162 optimal weight: 30.0000 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS H 44 GLN H 81 ASN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18226 Z= 0.221 Angle : 0.642 10.232 25843 Z= 0.370 Chirality : 0.038 0.165 2926 Planarity : 0.005 0.078 2271 Dihedral : 30.134 141.943 4754 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.43 (0.21), residues: 1394 helix: -0.38 (0.17), residues: 811 sheet: -1.41 (0.83), residues: 40 loop : -1.69 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 397 HIS 0.008 0.001 HIS G 82 PHE 0.020 0.001 PHE A 78 TYR 0.039 0.002 TYR H 37 ARG 0.007 0.001 ARG K 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6835 (m-80) cc_final: 0.6339 (m-80) REVERT: A 49 ARG cc_start: 0.8741 (ttm110) cc_final: 0.8358 (mmm-85) REVERT: A 120 MET cc_start: 0.8542 (mtp) cc_final: 0.8101 (mtp) REVERT: A 126 LEU cc_start: 0.9277 (tp) cc_final: 0.9044 (tp) REVERT: E 48 LEU cc_start: 0.9153 (tp) cc_final: 0.8628 (tp) REVERT: E 50 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7279 (tp30) REVERT: E 80 THR cc_start: 0.8346 (t) cc_final: 0.7671 (t) REVERT: E 93 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7923 (tm-30) REVERT: E 110 CYS cc_start: 0.8803 (m) cc_final: 0.8159 (m) REVERT: E 126 LEU cc_start: 0.9292 (tp) cc_final: 0.9058 (tt) REVERT: B 68 ASP cc_start: 0.8619 (m-30) cc_final: 0.6976 (m-30) REVERT: B 79 LYS cc_start: 0.8536 (mttp) cc_final: 0.8314 (mmtt) REVERT: B 92 ARG cc_start: 0.8090 (ptm-80) cc_final: 0.7485 (ttp-170) REVERT: B 100 PHE cc_start: 0.8857 (m-80) cc_final: 0.8646 (m-80) REVERT: F 27 GLN cc_start: 0.8946 (mm110) cc_final: 0.8461 (mp10) REVERT: F 46 ILE cc_start: 0.9244 (mt) cc_final: 0.9020 (mt) REVERT: F 88 TYR cc_start: 0.8350 (m-10) cc_final: 0.7671 (m-80) REVERT: C 85 LEU cc_start: 0.9344 (mt) cc_final: 0.8993 (tp) REVERT: C 94 ASN cc_start: 0.8808 (t0) cc_final: 0.8589 (t0) REVERT: G 19 ASN cc_start: 0.8840 (m-40) cc_final: 0.8368 (t0) REVERT: G 36 LYS cc_start: 0.9257 (mttt) cc_final: 0.8845 (mtpp) REVERT: G 38 ASN cc_start: 0.8845 (m110) cc_final: 0.8452 (m110) REVERT: G 64 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8631 (tm-30) REVERT: G 92 GLU cc_start: 0.7766 (tt0) cc_final: 0.7045 (tt0) REVERT: D 36 ILE cc_start: 0.8601 (pt) cc_final: 0.8394 (mp) REVERT: D 43 LYS cc_start: 0.9370 (mmtt) cc_final: 0.8571 (mtpp) REVERT: D 58 ILE cc_start: 0.9485 (mm) cc_final: 0.9214 (mm) REVERT: D 92 GLN cc_start: 0.8746 (tt0) cc_final: 0.7846 (tm-30) REVERT: D 93 THR cc_start: 0.9305 (m) cc_final: 0.8919 (p) REVERT: D 97 LEU cc_start: 0.9212 (tp) cc_final: 0.8816 (tp) REVERT: H 56 MET cc_start: 0.8489 (tpp) cc_final: 0.8228 (tpp) REVERT: H 64 ASN cc_start: 0.9067 (m-40) cc_final: 0.8155 (t0) REVERT: H 68 GLU cc_start: 0.8663 (tt0) cc_final: 0.8278 (tt0) REVERT: H 102 GLU cc_start: 0.8033 (tp30) cc_final: 0.7285 (tp30) REVERT: K 311 MSE cc_start: 0.5634 (mtp) cc_final: 0.5180 (mmm) REVERT: K 535 MSE cc_start: 0.5931 (mmp) cc_final: 0.5691 (mmm) REVERT: K 554 LEU cc_start: 0.3839 (pp) cc_final: 0.3429 (tp) REVERT: K 731 TYR cc_start: 0.5696 (m-80) cc_final: 0.5279 (m-80) REVERT: K 791 ASP cc_start: 0.6722 (t0) cc_final: 0.5338 (t0) REVERT: K 872 ARG cc_start: 0.0367 (mmt180) cc_final: -0.0578 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3369 time to fit residues: 135.9161 Evaluate side-chains 223 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 0.4980 chunk 159 optimal weight: 40.0000 chunk 78 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 125 GLN E 68 GLN E 125 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 79 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 668 ASN K 895 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 18226 Z= 0.347 Angle : 0.719 9.802 25843 Z= 0.404 Chirality : 0.041 0.198 2926 Planarity : 0.005 0.066 2271 Dihedral : 30.060 143.678 4754 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.02 (0.22), residues: 1394 helix: -0.02 (0.18), residues: 803 sheet: -1.51 (0.87), residues: 40 loop : -1.49 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 397 HIS 0.008 0.002 HIS G 31 PHE 0.033 0.002 PHE A 78 TYR 0.039 0.002 TYR H 37 ARG 0.019 0.001 ARG K 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8394 (tt0) cc_final: 0.8131 (tt0) REVERT: A 120 MET cc_start: 0.8668 (mtp) cc_final: 0.8261 (mtp) REVERT: E 50 GLU cc_start: 0.7882 (mm-30) cc_final: 0.6193 (tp30) REVERT: E 53 ARG cc_start: 0.8369 (ttt180) cc_final: 0.7984 (ttm170) REVERT: E 54 TYR cc_start: 0.9093 (m-10) cc_final: 0.8876 (m-10) REVERT: E 80 THR cc_start: 0.8308 (t) cc_final: 0.7418 (t) REVERT: E 93 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8014 (tm-30) REVERT: E 126 LEU cc_start: 0.9433 (tp) cc_final: 0.9095 (tt) REVERT: B 35 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7620 (ttm-80) REVERT: B 79 LYS cc_start: 0.8647 (mttp) cc_final: 0.8290 (mmtm) REVERT: F 46 ILE cc_start: 0.9331 (mt) cc_final: 0.9100 (mt) REVERT: F 63 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7855 (mm-30) REVERT: C 85 LEU cc_start: 0.9380 (mt) cc_final: 0.9141 (tt) REVERT: G 36 LYS cc_start: 0.9294 (mttt) cc_final: 0.8943 (mmmt) REVERT: G 38 ASN cc_start: 0.8949 (m110) cc_final: 0.8619 (m110) REVERT: G 92 GLU cc_start: 0.7832 (tt0) cc_final: 0.7353 (tt0) REVERT: D 43 LYS cc_start: 0.9408 (mmtt) cc_final: 0.8673 (mtpt) REVERT: H 64 ASN cc_start: 0.9155 (m-40) cc_final: 0.8204 (t0) REVERT: K 311 MSE cc_start: 0.5463 (mtp) cc_final: 0.5026 (mmm) REVERT: K 535 MSE cc_start: 0.6069 (mmp) cc_final: 0.5856 (mmm) REVERT: K 554 LEU cc_start: 0.3421 (pp) cc_final: 0.3020 (tp) REVERT: K 717 TYR cc_start: 0.5747 (t80) cc_final: 0.5058 (t80) REVERT: K 791 ASP cc_start: 0.6785 (t0) cc_final: 0.4916 (t70) REVERT: K 815 PHE cc_start: 0.6127 (p90) cc_final: 0.5810 (p90) REVERT: K 872 ARG cc_start: 0.0166 (mmt180) cc_final: -0.1220 (mmt90) outliers start: 1 outliers final: 1 residues processed: 237 average time/residue: 0.3300 time to fit residues: 112.7420 Evaluate side-chains 205 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 125 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 812 GLN K 875 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18226 Z= 0.373 Angle : 0.744 10.223 25843 Z= 0.416 Chirality : 0.042 0.171 2926 Planarity : 0.006 0.063 2271 Dihedral : 30.123 141.876 4754 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.95 (0.22), residues: 1394 helix: 0.01 (0.17), residues: 802 sheet: -1.93 (0.84), residues: 40 loop : -1.38 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 397 HIS 0.009 0.002 HIS F 75 PHE 0.038 0.003 PHE A 78 TYR 0.046 0.002 TYR H 37 ARG 0.009 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8337 (tt0) cc_final: 0.8131 (tt0) REVERT: A 120 MET cc_start: 0.8653 (mtp) cc_final: 0.8345 (mtp) REVERT: A 123 ASP cc_start: 0.8919 (m-30) cc_final: 0.8667 (m-30) REVERT: A 125 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8522 (tp40) REVERT: E 40 ARG cc_start: 0.6949 (ttm-80) cc_final: 0.6631 (ttt90) REVERT: E 50 GLU cc_start: 0.7980 (mm-30) cc_final: 0.6257 (tp30) REVERT: E 53 ARG cc_start: 0.8362 (ttt180) cc_final: 0.8001 (ttm170) REVERT: E 54 TYR cc_start: 0.9089 (m-10) cc_final: 0.8855 (m-10) REVERT: E 92 LEU cc_start: 0.9126 (tp) cc_final: 0.8920 (tp) REVERT: E 93 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8151 (tm-30) REVERT: E 105 GLU cc_start: 0.8647 (tt0) cc_final: 0.8402 (tt0) REVERT: E 133 GLU cc_start: 0.8963 (mp0) cc_final: 0.8710 (mp0) REVERT: B 35 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7771 (ttm-80) REVERT: B 79 LYS cc_start: 0.8681 (mttp) cc_final: 0.8326 (mmtt) REVERT: G 19 ASN cc_start: 0.8906 (m-40) cc_final: 0.8697 (m-40) REVERT: G 36 LYS cc_start: 0.9237 (mttt) cc_final: 0.8781 (mtpp) REVERT: G 38 ASN cc_start: 0.8985 (m110) cc_final: 0.8663 (m110) REVERT: G 83 LEU cc_start: 0.9361 (mm) cc_final: 0.9081 (mm) REVERT: G 92 GLU cc_start: 0.7863 (tt0) cc_final: 0.7465 (tt0) REVERT: D 38 ILE cc_start: 0.9670 (pt) cc_final: 0.9325 (pt) REVERT: D 39 TYR cc_start: 0.8577 (t80) cc_final: 0.8202 (t80) REVERT: D 43 LYS cc_start: 0.9423 (mmtt) cc_final: 0.8608 (mtpt) REVERT: D 90 GLU cc_start: 0.8879 (pt0) cc_final: 0.8570 (pt0) REVERT: D 96 ARG cc_start: 0.8822 (ptp-110) cc_final: 0.8130 (ptp90) REVERT: H 64 ASN cc_start: 0.9154 (m-40) cc_final: 0.8322 (t0) REVERT: K 256 MSE cc_start: 0.5368 (mtp) cc_final: 0.4735 (mtt) REVERT: K 311 MSE cc_start: 0.5314 (mtp) cc_final: 0.4846 (mmm) REVERT: K 535 MSE cc_start: 0.6159 (mmp) cc_final: 0.5856 (mmm) REVERT: K 554 LEU cc_start: 0.3458 (pp) cc_final: 0.2776 (tp) REVERT: K 815 PHE cc_start: 0.6052 (p90) cc_final: 0.5766 (p90) REVERT: K 875 GLN cc_start: 0.1702 (OUTLIER) cc_final: -0.1021 (mt0) outliers start: 2 outliers final: 0 residues processed: 242 average time/residue: 0.3211 time to fit residues: 112.7700 Evaluate side-chains 197 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 6.9990 chunk 143 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN H 44 GLN H 79 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 345 ASN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18226 Z= 0.302 Angle : 0.696 8.354 25843 Z= 0.391 Chirality : 0.040 0.185 2926 Planarity : 0.006 0.187 2271 Dihedral : 30.011 139.050 4754 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.16 % Allowed : 2.22 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.65 (0.22), residues: 1394 helix: 0.33 (0.18), residues: 797 sheet: -1.88 (0.85), residues: 40 loop : -1.36 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 397 HIS 0.006 0.001 HIS F 75 PHE 0.036 0.002 PHE K 454 TYR 0.018 0.002 TYR H 37 ARG 0.009 0.001 ARG K 640 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8384 (tt0) cc_final: 0.8138 (tt0) REVERT: A 120 MET cc_start: 0.8582 (mtp) cc_final: 0.8217 (mtp) REVERT: A 125 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8336 (tp40) REVERT: E 40 ARG cc_start: 0.7136 (ttm-80) cc_final: 0.6544 (ttt90) REVERT: E 50 GLU cc_start: 0.7950 (mm-30) cc_final: 0.6283 (tp30) REVERT: E 53 ARG cc_start: 0.8368 (ttt180) cc_final: 0.8038 (ttm170) REVERT: E 93 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8117 (tm-30) REVERT: E 120 MET cc_start: 0.9082 (mmm) cc_final: 0.8742 (mmp) REVERT: E 133 GLU cc_start: 0.8992 (mp0) cc_final: 0.8739 (mp0) REVERT: B 35 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7760 (ttm-80) REVERT: B 79 LYS cc_start: 0.8642 (mttp) cc_final: 0.8275 (mmtt) REVERT: B 84 MET cc_start: 0.8122 (mmp) cc_final: 0.7778 (mmm) REVERT: B 88 TYR cc_start: 0.8517 (m-10) cc_final: 0.8317 (m-10) REVERT: B 92 ARG cc_start: 0.8154 (ptm-80) cc_final: 0.7857 (tmt170) REVERT: F 26 ILE cc_start: 0.9479 (tp) cc_final: 0.9094 (tt) REVERT: F 27 GLN cc_start: 0.9072 (mm110) cc_final: 0.8734 (mp10) REVERT: C 56 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7829 (tm-30) REVERT: G 19 ASN cc_start: 0.8825 (m-40) cc_final: 0.8593 (t0) REVERT: G 29 ARG cc_start: 0.8492 (ttm170) cc_final: 0.7932 (ttm-80) REVERT: G 36 LYS cc_start: 0.9256 (mttt) cc_final: 0.8768 (mtpp) REVERT: G 38 ASN cc_start: 0.8942 (m110) cc_final: 0.8623 (m110) REVERT: G 71 ARG cc_start: 0.8886 (ttp-110) cc_final: 0.8665 (ttp80) REVERT: G 92 GLU cc_start: 0.7843 (tt0) cc_final: 0.7458 (tt0) REVERT: D 32 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7936 (tm-30) REVERT: D 43 LYS cc_start: 0.9442 (mmtt) cc_final: 0.8705 (mtpt) REVERT: D 96 ARG cc_start: 0.8754 (ptp-110) cc_final: 0.8379 (ptp90) REVERT: H 64 ASN cc_start: 0.9114 (m-40) cc_final: 0.8234 (t0) REVERT: K 256 MSE cc_start: 0.4933 (mtp) cc_final: 0.4370 (mtt) REVERT: K 311 MSE cc_start: 0.5332 (mtp) cc_final: 0.4909 (mmm) REVERT: K 466 TYR cc_start: 0.6163 (t80) cc_final: 0.5899 (t80) REVERT: K 535 MSE cc_start: 0.5824 (mmp) cc_final: 0.5419 (mmm) REVERT: K 554 LEU cc_start: 0.3372 (pp) cc_final: 0.2914 (tp) REVERT: K 872 ARG cc_start: 0.0303 (mmt180) cc_final: -0.1140 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 242 average time/residue: 0.3290 time to fit residues: 114.7953 Evaluate side-chains 200 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 9.9990 chunk 17 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 134 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 overall best weight: 5.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 552 ASN ** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 18226 Z= 0.382 Angle : 0.746 9.069 25843 Z= 0.419 Chirality : 0.043 0.168 2926 Planarity : 0.006 0.088 2271 Dihedral : 29.980 141.281 4754 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.81 (0.22), residues: 1394 helix: 0.11 (0.18), residues: 803 sheet: -1.89 (0.86), residues: 38 loop : -1.30 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 397 HIS 0.009 0.002 HIS F 75 PHE 0.043 0.003 PHE A 78 TYR 0.019 0.002 TYR H 37 ARG 0.007 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.9033 (m) cc_final: 0.8697 (m) REVERT: A 94 GLU cc_start: 0.8337 (tt0) cc_final: 0.8123 (tt0) REVERT: A 120 MET cc_start: 0.8615 (mtp) cc_final: 0.8278 (mtp) REVERT: A 125 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8326 (tp40) REVERT: E 40 ARG cc_start: 0.7125 (ttm-80) cc_final: 0.6809 (ttt90) REVERT: E 53 ARG cc_start: 0.8300 (ttt180) cc_final: 0.7738 (ttm170) REVERT: E 93 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8176 (tm-30) REVERT: E 120 MET cc_start: 0.9092 (mmm) cc_final: 0.8786 (mmp) REVERT: B 35 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7664 (ttm-80) REVERT: B 46 ILE cc_start: 0.9016 (mt) cc_final: 0.8815 (mm) REVERT: B 79 LYS cc_start: 0.8673 (mttp) cc_final: 0.8266 (mmtt) REVERT: B 84 MET cc_start: 0.8123 (mmp) cc_final: 0.7478 (mmm) REVERT: C 56 GLU cc_start: 0.8620 (mt-10) cc_final: 0.7864 (tm-30) REVERT: G 19 ASN cc_start: 0.8836 (m-40) cc_final: 0.8522 (t0) REVERT: G 24 GLN cc_start: 0.8077 (mp10) cc_final: 0.7775 (mp10) REVERT: G 36 LYS cc_start: 0.9247 (mttt) cc_final: 0.8794 (mmmt) REVERT: G 38 ASN cc_start: 0.8990 (m110) cc_final: 0.8682 (m110) REVERT: G 56 GLU cc_start: 0.8730 (mt-10) cc_final: 0.7813 (mt-10) REVERT: G 71 ARG cc_start: 0.8842 (ttp-110) cc_final: 0.8583 (ttp80) REVERT: G 92 GLU cc_start: 0.7857 (tt0) cc_final: 0.7477 (tt0) REVERT: D 38 ILE cc_start: 0.9604 (pt) cc_final: 0.9087 (tt) REVERT: D 43 LYS cc_start: 0.9436 (mmtt) cc_final: 0.8705 (mtpt) REVERT: D 96 ARG cc_start: 0.8760 (ptp-110) cc_final: 0.8263 (ptp90) REVERT: H 64 ASN cc_start: 0.9215 (m-40) cc_final: 0.8287 (t0) REVERT: K 245 MSE cc_start: 0.0725 (tpt) cc_final: 0.0259 (tpt) REVERT: K 256 MSE cc_start: 0.5068 (mtp) cc_final: 0.4403 (mtt) REVERT: K 283 LYS cc_start: 0.3850 (pttm) cc_final: 0.3191 (mmtt) REVERT: K 311 MSE cc_start: 0.5269 (mtp) cc_final: 0.4858 (mmm) REVERT: K 362 MSE cc_start: -0.4301 (ttt) cc_final: -0.4533 (ttt) REVERT: K 535 MSE cc_start: 0.5835 (mmp) cc_final: 0.5469 (mmm) REVERT: K 554 LEU cc_start: 0.3653 (pp) cc_final: 0.3152 (tp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3408 time to fit residues: 109.1186 Evaluate side-chains 187 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN G 73 ASN D 44 GLN H 79 HIS H 92 GLN K 510 GLN ** K 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18226 Z= 0.195 Angle : 0.640 7.898 25843 Z= 0.363 Chirality : 0.039 0.156 2926 Planarity : 0.004 0.062 2271 Dihedral : 29.878 135.698 4754 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.16 % Allowed : 1.15 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.37 (0.23), residues: 1394 helix: 0.50 (0.18), residues: 807 sheet: -2.11 (0.76), residues: 49 loop : -1.12 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 397 HIS 0.005 0.001 HIS G 82 PHE 0.029 0.002 PHE K 454 TYR 0.020 0.001 TYR H 37 ARG 0.011 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 251 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8366 (tt0) cc_final: 0.8156 (tt0) REVERT: A 120 MET cc_start: 0.8508 (mtp) cc_final: 0.8118 (mtp) REVERT: A 125 GLN cc_start: 0.8592 (tp-100) cc_final: 0.8277 (tp40) REVERT: E 40 ARG cc_start: 0.7147 (ttm-80) cc_final: 0.6906 (ttt90) REVERT: E 50 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8039 (mm-30) REVERT: E 53 ARG cc_start: 0.8410 (ttt180) cc_final: 0.7937 (ttp-170) REVERT: E 54 TYR cc_start: 0.8951 (m-10) cc_final: 0.8591 (m-10) REVERT: E 93 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8008 (tm-30) REVERT: E 94 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7518 (tm-30) REVERT: E 110 CYS cc_start: 0.8592 (m) cc_final: 0.7978 (m) REVERT: B 35 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7611 (ttm-80) REVERT: B 68 ASP cc_start: 0.8693 (m-30) cc_final: 0.7492 (m-30) REVERT: B 77 LYS cc_start: 0.9489 (mttt) cc_final: 0.8978 (mttp) REVERT: B 79 LYS cc_start: 0.8614 (mttp) cc_final: 0.8255 (mmtt) REVERT: B 92 ARG cc_start: 0.7981 (ptm-80) cc_final: 0.7596 (tmt170) REVERT: F 27 GLN cc_start: 0.8938 (mm110) cc_final: 0.8663 (mp10) REVERT: F 63 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7829 (mm-30) REVERT: F 65 VAL cc_start: 0.9621 (m) cc_final: 0.9317 (p) REVERT: C 56 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7752 (tm-30) REVERT: G 36 LYS cc_start: 0.9225 (mttt) cc_final: 0.8900 (mmmt) REVERT: G 38 ASN cc_start: 0.8780 (m110) cc_final: 0.8523 (m110) REVERT: G 56 GLU cc_start: 0.8730 (mt-10) cc_final: 0.7775 (mt-10) REVERT: G 71 ARG cc_start: 0.8840 (ttp-110) cc_final: 0.8631 (ttp80) REVERT: D 32 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7583 (tm-30) REVERT: D 43 LYS cc_start: 0.9381 (mmtt) cc_final: 0.8645 (mtpt) REVERT: D 96 ARG cc_start: 0.8693 (ptp-110) cc_final: 0.8273 (ptp90) REVERT: H 64 ASN cc_start: 0.9212 (m-40) cc_final: 0.8244 (t0) REVERT: H 92 GLN cc_start: 0.8536 (tm130) cc_final: 0.8321 (tm-30) REVERT: K 245 MSE cc_start: 0.0921 (tpt) cc_final: -0.0447 (tpt) REVERT: K 256 MSE cc_start: 0.5139 (mtp) cc_final: 0.4706 (mtt) REVERT: K 283 LYS cc_start: 0.3869 (pttm) cc_final: 0.3263 (mmtt) REVERT: K 311 MSE cc_start: 0.5279 (mtp) cc_final: 0.4853 (mmm) REVERT: K 362 MSE cc_start: -0.4165 (ttt) cc_final: -0.4460 (ttt) REVERT: K 535 MSE cc_start: 0.5718 (mmp) cc_final: 0.5482 (mmm) REVERT: K 712 MSE cc_start: 0.0501 (tpp) cc_final: 0.0083 (tpp) REVERT: K 872 ARG cc_start: 0.0745 (mmt180) cc_final: -0.0128 (mmt180) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.3372 time to fit residues: 122.2778 Evaluate side-chains 208 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 148 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 147 optimal weight: 0.0470 chunk 97 optimal weight: 7.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN H 44 GLN ** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN K 788 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18226 Z= 0.227 Angle : 0.647 7.955 25843 Z= 0.366 Chirality : 0.039 0.155 2926 Planarity : 0.005 0.067 2271 Dihedral : 29.681 135.664 4754 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.25 (0.23), residues: 1394 helix: 0.53 (0.18), residues: 811 sheet: -2.06 (0.80), residues: 45 loop : -0.98 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 397 HIS 0.003 0.001 HIS H 106 PHE 0.028 0.002 PHE K 454 TYR 0.016 0.002 TYR K 824 ARG 0.015 0.001 ARG K 640 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8559 (mtp) cc_final: 0.8088 (mtp) REVERT: A 125 GLN cc_start: 0.8662 (tp-100) cc_final: 0.8066 (tp40) REVERT: E 50 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8152 (mm-30) REVERT: E 53 ARG cc_start: 0.8407 (ttt180) cc_final: 0.8051 (ttt180) REVERT: E 54 TYR cc_start: 0.9038 (m-10) cc_final: 0.8757 (m-10) REVERT: E 93 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8059 (tm-30) REVERT: E 94 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7528 (tm-30) REVERT: E 120 MET cc_start: 0.9201 (mmm) cc_final: 0.8996 (mmp) REVERT: B 35 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7618 (ttm-80) REVERT: B 77 LYS cc_start: 0.9476 (mttt) cc_final: 0.9109 (mttp) REVERT: B 79 LYS cc_start: 0.8642 (mttp) cc_final: 0.8286 (mmtt) REVERT: B 92 ARG cc_start: 0.8053 (ptm-80) cc_final: 0.7740 (tmt170) REVERT: F 26 ILE cc_start: 0.9431 (tp) cc_final: 0.9103 (tp) REVERT: F 27 GLN cc_start: 0.8955 (mm110) cc_final: 0.8739 (mp10) REVERT: F 63 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7684 (mm-30) REVERT: C 56 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7719 (tm-30) REVERT: G 36 LYS cc_start: 0.9207 (mttt) cc_final: 0.8906 (mmmt) REVERT: G 38 ASN cc_start: 0.8714 (m110) cc_final: 0.8401 (m110) REVERT: D 43 LYS cc_start: 0.9380 (mmtt) cc_final: 0.8684 (mtpt) REVERT: D 59 MET cc_start: 0.8759 (mmm) cc_final: 0.8359 (mtt) REVERT: D 96 ARG cc_start: 0.8680 (ptp-110) cc_final: 0.8315 (ptp90) REVERT: H 64 ASN cc_start: 0.9040 (m-40) cc_final: 0.8302 (t0) REVERT: K 245 MSE cc_start: -0.0905 (tpt) cc_final: -0.1551 (tpt) REVERT: K 247 ARG cc_start: 0.7224 (ttm-80) cc_final: 0.6717 (ptt-90) REVERT: K 256 MSE cc_start: 0.5152 (mtp) cc_final: 0.4605 (mtt) REVERT: K 311 MSE cc_start: 0.5335 (mtp) cc_final: 0.4926 (mmm) REVERT: K 362 MSE cc_start: -0.4341 (ttt) cc_final: -0.4639 (ttt) REVERT: K 535 MSE cc_start: 0.5457 (mmp) cc_final: 0.5202 (mmm) REVERT: K 786 PHE cc_start: 0.6133 (t80) cc_final: 0.5887 (t80) REVERT: K 872 ARG cc_start: 0.0615 (mmt180) cc_final: -0.0662 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3389 time to fit residues: 119.2568 Evaluate side-chains 201 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 164 optimal weight: 0.1980 chunk 151 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18226 Z= 0.321 Angle : 0.709 8.637 25843 Z= 0.397 Chirality : 0.041 0.262 2926 Planarity : 0.005 0.067 2271 Dihedral : 29.699 138.638 4754 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.08 % Allowed : 0.66 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.49 (0.22), residues: 1394 helix: 0.30 (0.18), residues: 809 sheet: -2.05 (0.81), residues: 45 loop : -1.01 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 397 HIS 0.009 0.001 HIS G 31 PHE 0.031 0.002 PHE K 726 TYR 0.018 0.002 TYR D 80 ARG 0.006 0.001 ARG K 602 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8221 (tp40) REVERT: E 50 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8005 (mm-30) REVERT: E 53 ARG cc_start: 0.8429 (ttt180) cc_final: 0.7870 (ttt180) REVERT: E 93 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 94 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7589 (tm-30) REVERT: E 120 MET cc_start: 0.9206 (mmm) cc_final: 0.8820 (mmp) REVERT: E 133 GLU cc_start: 0.8191 (mp0) cc_final: 0.7802 (mp0) REVERT: B 35 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7599 (ttm-80) REVERT: B 79 LYS cc_start: 0.8658 (mttp) cc_final: 0.8299 (mmtt) REVERT: B 92 ARG cc_start: 0.8156 (ptm-80) cc_final: 0.7859 (tmt170) REVERT: F 27 GLN cc_start: 0.9029 (mm110) cc_final: 0.8698 (mp10) REVERT: F 63 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7870 (mm-30) REVERT: C 56 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7695 (tm-30) REVERT: G 36 LYS cc_start: 0.9204 (mttt) cc_final: 0.8760 (mmmt) REVERT: G 38 ASN cc_start: 0.8879 (m110) cc_final: 0.8600 (m110) REVERT: G 91 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6812 (tm-30) REVERT: G 92 GLU cc_start: 0.7930 (tt0) cc_final: 0.7605 (mm-30) REVERT: D 38 ILE cc_start: 0.9624 (pt) cc_final: 0.9116 (tt) REVERT: D 43 LYS cc_start: 0.9395 (mmtt) cc_final: 0.8718 (mtpt) REVERT: D 96 ARG cc_start: 0.8698 (ptp-110) cc_final: 0.8297 (ptp90) REVERT: H 64 ASN cc_start: 0.9215 (m-40) cc_final: 0.8417 (t0) REVERT: K 247 ARG cc_start: 0.7193 (ttm-80) cc_final: 0.6634 (ptt-90) REVERT: K 256 MSE cc_start: 0.5118 (mtp) cc_final: 0.4729 (mtt) REVERT: K 267 MSE cc_start: 0.3889 (tmm) cc_final: 0.3430 (tmm) REVERT: K 283 LYS cc_start: 0.4130 (pttm) cc_final: 0.3409 (mmtt) REVERT: K 311 MSE cc_start: 0.5581 (mtp) cc_final: 0.5041 (mmm) REVERT: K 535 MSE cc_start: 0.5608 (mmp) cc_final: 0.5307 (mmm) REVERT: K 712 MSE cc_start: 0.0364 (tpp) cc_final: -0.0152 (tpp) REVERT: K 872 ARG cc_start: 0.0755 (mmt180) cc_final: -0.0638 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.3456 time to fit residues: 116.0113 Evaluate side-chains 191 residues out of total 1216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.101968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072871 restraints weight = 75772.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071990 restraints weight = 50442.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073188 restraints weight = 42679.694| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18226 Z= 0.209 Angle : 0.644 8.774 25843 Z= 0.363 Chirality : 0.039 0.200 2926 Planarity : 0.005 0.068 2271 Dihedral : 29.565 135.613 4754 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.19 (0.23), residues: 1394 helix: 0.54 (0.18), residues: 807 sheet: -1.90 (0.81), residues: 45 loop : -0.88 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 397 HIS 0.005 0.001 HIS G 31 PHE 0.026 0.002 PHE K 454 TYR 0.015 0.001 TYR C 57 ARG 0.010 0.001 ARG K 705 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3230.45 seconds wall clock time: 58 minutes 36.48 seconds (3516.48 seconds total)