Starting phenix.real_space_refine on Thu Feb 5 10:21:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xyf_33520/02_2026/7xyf_33520.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xyf_33520/02_2026/7xyf_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xyf_33520/02_2026/7xyf_33520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xyf_33520/02_2026/7xyf_33520.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xyf_33520/02_2026/7xyf_33520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xyf_33520/02_2026/7xyf_33520.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 3.56, per 1000 atoms: 0.21 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: 1.24 Conformation dependent library (CDL) restraints added in 538.8 milliseconds 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: 2.73 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: 4.54 Time building geometry restraints manager: 1.76 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: 25040 2.30 - 4.61: 725 4.61 - 6.91: 64 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: 0.970 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.030 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.870 ------------------------------------------------------------------------------- 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= 0.387 Angle : 0.930 11.516 25843 Z= 0.543 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 : 13.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (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 ARG 0.012 0.001 ARG K 495 TYR 0.014 0.002 TYR K 731 PHE 0.028 0.003 PHE K 832 TRP 0.013 0.003 TRP K 757 HIS 0.015 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00832 (18226) covalent geometry : angle 0.93023 (25843) hydrogen bonds : bond 0.31582 ( 837) hydrogen bonds : angle 10.02553 ( 2092) *********************** 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 to be fit. rotamer outliers: 26 poor density : 342 time to evaluate : 0.518 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: 0.9130 (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: -0.1429 (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: 0.4665 (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: 0.1796 time to fit residues: 85.4948 Evaluate side-chains 243 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 231 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 H 81 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.101467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.072917 restraints weight = 76013.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071105 restraints weight = 52894.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.071999 restraints weight = 45762.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072157 restraints weight = 31602.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072104 restraints weight = 33527.576| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18226 Z= 0.220 Angle : 0.706 7.722 25843 Z= 0.407 Chirality : 0.041 0.182 2926 Planarity : 0.006 0.072 2271 Dihedral : 30.588 140.157 4754 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.19), residues: 1394 helix: -1.64 (0.15), residues: 812 sheet: -1.67 (0.79), residues: 40 loop : -1.98 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.042 0.002 TYR H 37 PHE 0.023 0.002 PHE A 78 TRP 0.010 0.002 TRP K 397 HIS 0.012 0.002 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00479 (18226) covalent geometry : angle 0.70588 (25843) hydrogen bonds : bond 0.08487 ( 837) hydrogen bonds : angle 4.69465 ( 2092) *********************** 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 291 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.398 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 49 ARG cc_start: 0.8551 (ttm110) cc_final: 0.8216 (mmm-85) REVERT: A 53 ARG cc_start: 0.8453 (ttt180) cc_final: 0.8179 (tpt-90) REVERT: A 120 MET cc_start: 0.8680 (mtp) cc_final: 0.8386 (mtp) REVERT: A 126 LEU cc_start: 0.9319 (tp) cc_final: 0.9108 (tp) REVERT: A 129 ARG cc_start: 0.8578 (ttt90) cc_final: 0.8356 (tpp80) REVERT: E 48 LEU cc_start: 0.9228 (tp) cc_final: 0.8727 (tp) REVERT: E 50 GLU cc_start: 0.7893 (mm-30) cc_final: 0.6725 (tp30) REVERT: E 54 TYR cc_start: 0.8878 (m-10) cc_final: 0.8517 (m-10) REVERT: E 110 CYS cc_start: 0.8724 (m) cc_final: 0.8037 (m) REVERT: E 126 LEU cc_start: 0.9447 (tp) cc_final: 0.9079 (tt) REVERT: B 54 THR cc_start: 0.8891 (p) cc_final: 0.8620 (m) REVERT: B 84 MET cc_start: 0.7887 (tpp) cc_final: 0.7546 (tpp) REVERT: F 63 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7905 (mm-30) REVERT: F 88 TYR cc_start: 0.8379 (m-10) cc_final: 0.7639 (m-80) REVERT: G 36 LYS cc_start: 0.9033 (mttt) cc_final: 0.8781 (mtpp) REVERT: G 38 ASN cc_start: 0.8793 (m110) cc_final: 0.8592 (m110) REVERT: G 84 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8534 (tp-100) REVERT: G 92 GLU cc_start: 0.7894 (tt0) cc_final: 0.7566 (tt0) REVERT: D 43 LYS cc_start: 0.9346 (mmtt) cc_final: 0.8684 (mtpt) REVERT: D 92 GLN cc_start: 0.8582 (tt0) cc_final: 0.7949 (tm-30) REVERT: D 93 THR cc_start: 0.9215 (m) cc_final: 0.8979 (p) REVERT: D 96 ARG cc_start: 0.8326 (mtt180) cc_final: 0.8041 (ttm110) REVERT: D 110 GLU cc_start: 0.8134 (tp30) cc_final: 0.7890 (tm-30) REVERT: H 64 ASN cc_start: 0.8928 (m-40) cc_final: 0.8085 (t0) REVERT: K 245 MSE cc_start: 0.0772 (tpt) cc_final: 0.0279 (tpt) REVERT: K 311 MSE cc_start: 0.5278 (mtp) cc_final: 0.3049 (tmm) REVERT: K 535 MSE cc_start: 0.6253 (mmp) cc_final: 0.5689 (mmm) REVERT: K 582 MSE cc_start: 0.4671 (mtm) cc_final: -0.3710 (ttp) REVERT: K 724 TYR cc_start: 0.7270 (m-10) cc_final: 0.6982 (m-10) REVERT: K 872 ARG cc_start: 0.0246 (mmt180) cc_final: -0.0654 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1492 time to fit residues: 62.1025 Evaluate side-chains 220 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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: 8.9990 chunk 146 optimal weight: 0.0170 chunk 91 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 93 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 75 HIS C 24 GLN D 44 GLN D 106 HIS H 44 GLN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 875 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.102258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.073970 restraints weight = 76360.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.072471 restraints weight = 52308.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.073273 restraints weight = 45246.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.073406 restraints weight = 32057.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.073429 restraints weight = 30209.546| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3599 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= 0.183 Angle : 0.648 10.363 25843 Z= 0.373 Chirality : 0.039 0.164 2926 Planarity : 0.005 0.067 2271 Dihedral : 30.138 142.025 4754 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.08 % Allowed : 3.79 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.21), residues: 1394 helix: -0.43 (0.17), residues: 806 sheet: -1.35 (0.85), residues: 40 loop : -1.72 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 35 TYR 0.038 0.002 TYR H 37 PHE 0.021 0.001 PHE A 78 TRP 0.013 0.002 TRP K 397 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00400 (18226) covalent geometry : angle 0.64823 (25843) hydrogen bonds : bond 0.07379 ( 837) hydrogen bonds : angle 4.13987 ( 2092) *********************** 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 266 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.427 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 41 TYR cc_start: 0.6555 (m-80) cc_final: 0.6148 (m-80) REVERT: A 94 GLU cc_start: 0.8133 (tt0) cc_final: 0.7737 (tt0) REVERT: A 120 MET cc_start: 0.8626 (mtp) cc_final: 0.8203 (mtp) REVERT: A 126 LEU cc_start: 0.9346 (tp) cc_final: 0.9143 (tp) REVERT: A 129 ARG cc_start: 0.8539 (ttt90) cc_final: 0.8008 (ttp80) REVERT: E 48 LEU cc_start: 0.9265 (tp) cc_final: 0.8765 (tp) REVERT: E 93 GLN cc_start: 0.8825 (tt0) cc_final: 0.8596 (tm-30) REVERT: E 110 CYS cc_start: 0.8622 (m) cc_final: 0.8142 (m) REVERT: E 120 MET cc_start: 0.8831 (mmm) cc_final: 0.8573 (mmm) REVERT: E 126 LEU cc_start: 0.9327 (tp) cc_final: 0.8983 (tt) REVERT: B 68 ASP cc_start: 0.8484 (m-30) cc_final: 0.6915 (m-30) REVERT: B 92 ARG cc_start: 0.7951 (ptm-80) cc_final: 0.7430 (ttp-170) REVERT: F 27 GLN cc_start: 0.8866 (mm110) cc_final: 0.8467 (mp10) REVERT: F 46 ILE cc_start: 0.9271 (mt) cc_final: 0.9006 (mt) REVERT: F 88 TYR cc_start: 0.8318 (m-10) cc_final: 0.7580 (m-80) REVERT: C 85 LEU cc_start: 0.9274 (mt) cc_final: 0.8975 (tp) REVERT: G 19 ASN cc_start: 0.8682 (m-40) cc_final: 0.8324 (t0) REVERT: G 36 LYS cc_start: 0.9028 (mttt) cc_final: 0.8739 (mtpp) REVERT: G 92 GLU cc_start: 0.7668 (tt0) cc_final: 0.7019 (tt0) REVERT: D 36 ILE cc_start: 0.8546 (pt) cc_final: 0.8216 (mp) REVERT: D 43 LYS cc_start: 0.9342 (mmtt) cc_final: 0.8668 (mtpt) REVERT: D 58 ILE cc_start: 0.9485 (mm) cc_final: 0.9224 (mm) REVERT: D 97 LEU cc_start: 0.9204 (tp) cc_final: 0.8849 (tp) REVERT: H 56 MET cc_start: 0.8342 (tpp) cc_final: 0.8096 (tpp) REVERT: H 64 ASN cc_start: 0.9040 (m-40) cc_final: 0.8123 (t0) REVERT: H 102 GLU cc_start: 0.7672 (tp30) cc_final: 0.6989 (tp30) REVERT: K 311 MSE cc_start: 0.5573 (mtp) cc_final: 0.4940 (mmm) REVERT: K 535 MSE cc_start: 0.6575 (mmp) cc_final: 0.6233 (mmm) REVERT: K 554 LEU cc_start: 0.3624 (pp) cc_final: 0.3155 (tp) REVERT: K 724 TYR cc_start: 0.7041 (m-10) cc_final: 0.6712 (m-10) REVERT: K 875 GLN cc_start: 0.1780 (OUTLIER) cc_final: -0.1526 (mt0) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.1516 time to fit residues: 57.9549 Evaluate side-chains 210 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 102 optimal weight: 0.0060 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 79 HIS K 668 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.102801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073258 restraints weight = 76648.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.072368 restraints weight = 50451.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.073247 restraints weight = 41026.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.073461 restraints weight = 29157.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.073672 restraints weight = 26070.869| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18226 Z= 0.161 Angle : 0.618 10.472 25843 Z= 0.354 Chirality : 0.038 0.146 2926 Planarity : 0.005 0.094 2271 Dihedral : 29.900 139.184 4754 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.08 % Allowed : 3.54 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.22), residues: 1394 helix: 0.19 (0.18), residues: 810 sheet: -1.28 (0.86), residues: 40 loop : -1.55 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 305 TYR 0.035 0.002 TYR H 37 PHE 0.014 0.001 PHE K 832 TRP 0.016 0.001 TRP K 397 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00351 (18226) covalent geometry : angle 0.61775 (25843) hydrogen bonds : bond 0.07026 ( 837) hydrogen bonds : angle 3.86466 ( 2092) *********************** 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 261 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.494 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: 0.8191 (tt0) cc_final: 0.7954 (tt0) REVERT: A 120 MET cc_start: 0.8699 (mtp) cc_final: 0.8228 (mtp) REVERT: A 126 LEU cc_start: 0.9309 (tp) cc_final: 0.9092 (tt) REVERT: E 50 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7797 (mm-30) REVERT: E 54 TYR cc_start: 0.8922 (m-10) cc_final: 0.8550 (m-10) REVERT: E 80 THR cc_start: 0.8421 (t) cc_final: 0.7524 (t) REVERT: E 93 GLN cc_start: 0.8898 (tt0) cc_final: 0.8460 (tm-30) REVERT: E 94 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7600 (tm-30) REVERT: E 110 CYS cc_start: 0.8692 (m) cc_final: 0.8126 (m) REVERT: E 126 LEU cc_start: 0.9288 (tp) cc_final: 0.8894 (tt) REVERT: B 35 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7453 (ttm-80) REVERT: F 27 GLN cc_start: 0.8925 (mm110) cc_final: 0.8476 (mp10) REVERT: F 46 ILE cc_start: 0.9272 (mt) cc_final: 0.8978 (mt) REVERT: F 63 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7964 (mm-30) REVERT: C 56 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7426 (tm-30) REVERT: C 85 LEU cc_start: 0.9281 (mt) cc_final: 0.9042 (tt) REVERT: G 19 ASN cc_start: 0.8669 (m-40) cc_final: 0.8298 (t0) REVERT: G 36 LYS cc_start: 0.9146 (mttt) cc_final: 0.8867 (mmmt) REVERT: G 38 ASN cc_start: 0.8738 (m110) cc_final: 0.8453 (m110) REVERT: G 92 GLU cc_start: 0.7688 (tt0) cc_final: 0.7029 (tt0) REVERT: G 102 ILE cc_start: 0.9640 (mm) cc_final: 0.9364 (mm) REVERT: D 31 LYS cc_start: 0.8718 (tttm) cc_final: 0.8502 (tttm) REVERT: D 36 ILE cc_start: 0.8529 (pt) cc_final: 0.8203 (mp) REVERT: D 43 LYS cc_start: 0.9299 (mmtt) cc_final: 0.8483 (mtpp) REVERT: D 58 ILE cc_start: 0.9415 (mm) cc_final: 0.9133 (mm) REVERT: D 92 GLN cc_start: 0.8495 (tt0) cc_final: 0.8049 (tm-30) REVERT: D 93 THR cc_start: 0.9166 (p) cc_final: 0.8637 (p) REVERT: H 56 MET cc_start: 0.8433 (tpp) cc_final: 0.8169 (tpp) REVERT: H 64 ASN cc_start: 0.9013 (m-40) cc_final: 0.8202 (t0) REVERT: H 102 GLU cc_start: 0.7639 (tp30) cc_final: 0.6943 (tp30) REVERT: K 245 MSE cc_start: 0.0706 (tpt) cc_final: 0.0352 (tpt) REVERT: K 311 MSE cc_start: 0.5478 (mtp) cc_final: 0.4744 (mmm) REVERT: K 554 LEU cc_start: 0.3500 (pp) cc_final: 0.2976 (tp) REVERT: K 872 ARG cc_start: 0.0206 (mmm160) cc_final: -0.1132 (mmt90) REVERT: K 892 GLU cc_start: 0.5109 (tp30) cc_final: 0.4823 (tt0) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.1302 time to fit residues: 50.1818 Evaluate side-chains 214 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 19 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 44 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 812 GLN K 895 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.099313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071339 restraints weight = 75862.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070000 restraints weight = 55396.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070169 restraints weight = 42847.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.070495 restraints weight = 38519.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070218 restraints weight = 35342.849| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 18226 Z= 0.311 Angle : 0.750 9.820 25843 Z= 0.422 Chirality : 0.043 0.166 2926 Planarity : 0.006 0.079 2271 Dihedral : 30.050 144.429 4754 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.22), residues: 1394 helix: 0.11 (0.18), residues: 808 sheet: -2.01 (0.78), residues: 45 loop : -1.30 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 40 TYR 0.041 0.002 TYR H 37 PHE 0.025 0.002 PHE K 610 TRP 0.018 0.002 TRP K 450 HIS 0.008 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00683 (18226) covalent geometry : angle 0.74989 (25843) hydrogen bonds : bond 0.07768 ( 837) hydrogen bonds : angle 4.45322 ( 2092) *********************** 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 238 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.497 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: 0.8224 (tt0) cc_final: 0.7982 (tt0) REVERT: A 120 MET cc_start: 0.8761 (mtp) cc_final: 0.8477 (mtp) REVERT: A 123 ASP cc_start: 0.9111 (m-30) cc_final: 0.8886 (m-30) REVERT: E 50 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7834 (mm-30) REVERT: E 80 THR cc_start: 0.8190 (t) cc_final: 0.7760 (p) REVERT: E 81 ASP cc_start: 0.8042 (m-30) cc_final: 0.7736 (m-30) REVERT: E 93 GLN cc_start: 0.8802 (tt0) cc_final: 0.8445 (tm-30) REVERT: B 35 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7670 (ttm-80) REVERT: G 36 LYS cc_start: 0.9179 (mttt) cc_final: 0.8834 (mmmt) REVERT: G 38 ASN cc_start: 0.9113 (m110) cc_final: 0.8708 (m110) REVERT: G 83 LEU cc_start: 0.9290 (mm) cc_final: 0.9079 (mm) REVERT: G 92 GLU cc_start: 0.7911 (tt0) cc_final: 0.7360 (tt0) REVERT: D 36 ILE cc_start: 0.8876 (pt) cc_final: 0.8584 (mp) REVERT: D 38 ILE cc_start: 0.9623 (pt) cc_final: 0.9020 (tt) REVERT: D 43 LYS cc_start: 0.9337 (mmtt) cc_final: 0.8539 (mtpt) REVERT: D 92 GLN cc_start: 0.8563 (tt0) cc_final: 0.8271 (tm-30) REVERT: D 93 THR cc_start: 0.9223 (p) cc_final: 0.8843 (p) REVERT: H 64 ASN cc_start: 0.9046 (m-40) cc_final: 0.8261 (t0) REVERT: K 256 MSE cc_start: 0.5036 (mtp) cc_final: 0.4250 (mtt) REVERT: K 311 MSE cc_start: 0.5633 (mtp) cc_final: 0.5132 (mmm) REVERT: K 535 MSE cc_start: 0.6502 (mmm) cc_final: 0.5918 (mmm) REVERT: K 554 LEU cc_start: 0.3347 (pp) cc_final: 0.2898 (tp) REVERT: K 607 MSE cc_start: 0.2856 (mtm) cc_final: 0.2234 (mtm) REVERT: K 815 PHE cc_start: 0.6380 (p90) cc_final: 0.6083 (p90) REVERT: K 872 ARG cc_start: 0.1014 (mmt180) cc_final: 0.0367 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1248 time to fit residues: 44.2330 Evaluate side-chains 200 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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** G 110 ASN D 46 HIS H 44 GLN H 79 HIS H 92 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.102474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072837 restraints weight = 75011.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.071950 restraints weight = 52952.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.072960 restraints weight = 38565.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.073258 restraints weight = 29828.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073049 restraints weight = 24521.986| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18226 Z= 0.165 Angle : 0.632 10.625 25843 Z= 0.361 Chirality : 0.038 0.148 2926 Planarity : 0.005 0.062 2271 Dihedral : 29.885 136.169 4754 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.08 % Allowed : 2.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1394 helix: 0.50 (0.18), residues: 811 sheet: -1.84 (0.80), residues: 45 loop : -1.18 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 40 TYR 0.017 0.002 TYR F 98 PHE 0.029 0.002 PHE K 832 TRP 0.016 0.001 TRP K 397 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00364 (18226) covalent geometry : angle 0.63159 (25843) hydrogen bonds : bond 0.06873 ( 837) hydrogen bonds : angle 3.87859 ( 2092) *********************** 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 259 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9299 (mm) cc_final: 0.9037 (mm) REVERT: A 120 MET cc_start: 0.8701 (mtp) cc_final: 0.8316 (mtp) REVERT: A 123 ASP cc_start: 0.9029 (m-30) cc_final: 0.8811 (m-30) REVERT: E 50 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7810 (mm-30) REVERT: E 92 LEU cc_start: 0.9237 (tp) cc_final: 0.9015 (tp) REVERT: E 93 GLN cc_start: 0.8867 (tt0) cc_final: 0.8345 (tm-30) REVERT: B 35 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7611 (ttm-80) REVERT: F 26 ILE cc_start: 0.9431 (tp) cc_final: 0.9045 (tt) REVERT: F 27 GLN cc_start: 0.8974 (mm110) cc_final: 0.8663 (mp10) REVERT: F 46 ILE cc_start: 0.9311 (mt) cc_final: 0.9027 (mt) REVERT: F 59 LYS cc_start: 0.9331 (ttmm) cc_final: 0.9068 (tppp) REVERT: F 93 GLN cc_start: 0.8231 (mp10) cc_final: 0.7986 (mp10) REVERT: C 56 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7704 (tm-30) REVERT: G 36 LYS cc_start: 0.9133 (mttt) cc_final: 0.8814 (mmmt) REVERT: G 38 ASN cc_start: 0.8856 (m110) cc_final: 0.8437 (m110) REVERT: G 92 GLU cc_start: 0.7767 (tt0) cc_final: 0.7184 (tt0) REVERT: D 36 ILE cc_start: 0.8753 (pt) cc_final: 0.8165 (mm) REVERT: D 38 ILE cc_start: 0.9653 (pt) cc_final: 0.9277 (tt) REVERT: D 43 LYS cc_start: 0.9341 (mmtt) cc_final: 0.8567 (mtpt) REVERT: D 92 GLN cc_start: 0.8600 (tt0) cc_final: 0.8166 (tm-30) REVERT: D 93 THR cc_start: 0.9345 (p) cc_final: 0.8672 (p) REVERT: D 96 ARG cc_start: 0.8291 (ptp-170) cc_final: 0.8070 (ptp-170) REVERT: H 64 ASN cc_start: 0.9053 (m-40) cc_final: 0.8163 (t0) REVERT: K 256 MSE cc_start: 0.5750 (mtp) cc_final: 0.5286 (mtt) REVERT: K 283 LYS cc_start: 0.2616 (pttm) cc_final: 0.2186 (tptm) REVERT: K 311 MSE cc_start: 0.5384 (mtp) cc_final: 0.4541 (mmm) REVERT: K 314 MSE cc_start: 0.4698 (ttp) cc_final: 0.4014 (ptm) REVERT: K 535 MSE cc_start: 0.6757 (mmm) cc_final: 0.6197 (mmm) REVERT: K 554 LEU cc_start: 0.3594 (pp) cc_final: 0.3070 (tp) REVERT: K 729 MSE cc_start: 0.3648 (tpt) cc_final: 0.3022 (tpp) REVERT: K 815 PHE cc_start: 0.6576 (p90) cc_final: 0.6357 (p90) REVERT: K 872 ARG cc_start: 0.0959 (mmt180) cc_final: 0.0055 (mmt90) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.1271 time to fit residues: 48.5846 Evaluate side-chains 203 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 chunk 119 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 44 GLN K 739 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.101964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072927 restraints weight = 75164.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071263 restraints weight = 51826.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072371 restraints weight = 39238.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072351 restraints weight = 29711.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.072648 restraints weight = 27540.126| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18226 Z= 0.184 Angle : 0.642 9.062 25843 Z= 0.364 Chirality : 0.038 0.167 2926 Planarity : 0.005 0.106 2271 Dihedral : 29.748 137.514 4754 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1394 helix: 0.64 (0.18), residues: 806 sheet: -1.81 (0.76), residues: 49 loop : -1.10 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 40 TYR 0.014 0.002 TYR H 37 PHE 0.026 0.001 PHE K 832 TRP 0.015 0.001 TRP K 397 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00408 (18226) covalent geometry : angle 0.64239 (25843) hydrogen bonds : bond 0.06846 ( 837) hydrogen bonds : angle 3.88074 ( 2092) *********************** 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 243 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8733 (mtp) cc_final: 0.8354 (mtp) REVERT: E 50 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7788 (mm-30) REVERT: E 93 GLN cc_start: 0.8845 (tt0) cc_final: 0.8428 (tm-30) REVERT: E 120 MET cc_start: 0.9043 (mmm) cc_final: 0.8726 (mmp) REVERT: B 35 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7606 (ttm-80) REVERT: B 79 LYS cc_start: 0.7953 (tppt) cc_final: 0.7741 (tppt) REVERT: B 84 MET cc_start: 0.7763 (tpt) cc_final: 0.7517 (tpp) REVERT: F 26 ILE cc_start: 0.9427 (tp) cc_final: 0.9050 (tt) REVERT: F 27 GLN cc_start: 0.8953 (mm110) cc_final: 0.8690 (mp10) REVERT: F 46 ILE cc_start: 0.9318 (mt) cc_final: 0.9037 (mt) REVERT: F 59 LYS cc_start: 0.9294 (ttmm) cc_final: 0.9055 (tppp) REVERT: C 55 MET cc_start: 0.7931 (mtm) cc_final: 0.7678 (mtm) REVERT: C 56 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7847 (tm-30) REVERT: G 36 LYS cc_start: 0.9170 (mttt) cc_final: 0.8839 (mmmt) REVERT: G 38 ASN cc_start: 0.8794 (m110) cc_final: 0.8414 (m110) REVERT: G 92 GLU cc_start: 0.7660 (tt0) cc_final: 0.7060 (tt0) REVERT: D 36 ILE cc_start: 0.8692 (pt) cc_final: 0.8215 (mm) REVERT: D 38 ILE cc_start: 0.9695 (pt) cc_final: 0.9328 (tt) REVERT: D 43 LYS cc_start: 0.9326 (mmtt) cc_final: 0.8565 (mtpt) REVERT: D 76 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.7937 (mmm-85) REVERT: D 92 GLN cc_start: 0.8567 (tt0) cc_final: 0.8135 (tm-30) REVERT: D 93 THR cc_start: 0.9307 (p) cc_final: 0.8640 (p) REVERT: D 96 ARG cc_start: 0.8301 (ptp-170) cc_final: 0.8058 (ptp-170) REVERT: H 56 MET cc_start: 0.8384 (tpp) cc_final: 0.8163 (tpp) REVERT: H 64 ASN cc_start: 0.9071 (m-40) cc_final: 0.8283 (t0) REVERT: K 256 MSE cc_start: 0.5693 (mtp) cc_final: 0.5197 (mtt) REVERT: K 283 LYS cc_start: 0.3759 (pttm) cc_final: 0.3249 (tptt) REVERT: K 311 MSE cc_start: 0.5372 (mtp) cc_final: 0.4462 (mmm) REVERT: K 314 MSE cc_start: 0.4627 (ttp) cc_final: 0.3852 (ptm) REVERT: K 466 TYR cc_start: 0.6693 (t80) cc_final: 0.6043 (t80) REVERT: K 535 MSE cc_start: 0.6548 (mmm) cc_final: 0.5987 (mmm) REVERT: K 815 PHE cc_start: 0.6555 (p90) cc_final: 0.6323 (p90) REVERT: K 872 ARG cc_start: 0.0741 (mmt180) cc_final: -0.0190 (mmt90) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1189 time to fit residues: 42.9431 Evaluate side-chains 199 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 128 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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** G 110 ASN H 44 GLN H 79 HIS H 92 GLN K 510 GLN ** K 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.100509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072418 restraints weight = 76243.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070867 restraints weight = 60628.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071601 restraints weight = 46237.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.071770 restraints weight = 35631.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.071543 restraints weight = 33910.250| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4967 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= 0.237 Angle : 0.676 8.749 25843 Z= 0.382 Chirality : 0.040 0.156 2926 Planarity : 0.005 0.063 2271 Dihedral : 29.753 139.170 4754 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.08 % Allowed : 0.91 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1394 helix: 0.62 (0.18), residues: 800 sheet: -1.94 (0.82), residues: 45 loop : -1.02 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 42 TYR 0.021 0.002 TYR K 487 PHE 0.022 0.002 PHE K 832 TRP 0.014 0.002 TRP K 397 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00528 (18226) covalent geometry : angle 0.67598 (25843) hydrogen bonds : bond 0.07061 ( 837) hydrogen bonds : angle 4.14769 ( 2092) *********************** 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 239 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8772 (mtp) cc_final: 0.8359 (mtp) REVERT: E 50 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7714 (mm-30) REVERT: E 54 TYR cc_start: 0.9078 (m-10) cc_final: 0.8715 (m-10) REVERT: E 93 GLN cc_start: 0.8861 (tt0) cc_final: 0.8417 (tm-30) REVERT: E 120 MET cc_start: 0.8995 (mmm) cc_final: 0.8691 (mmp) REVERT: E 133 GLU cc_start: 0.8857 (mp0) cc_final: 0.8619 (mp0) REVERT: B 35 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7558 (ttm-80) REVERT: B 46 ILE cc_start: 0.9048 (mt) cc_final: 0.8783 (mm) REVERT: B 84 MET cc_start: 0.7859 (tpt) cc_final: 0.7498 (tpp) REVERT: B 92 ARG cc_start: 0.7868 (ptm-80) cc_final: 0.7431 (ttp-170) REVERT: F 26 ILE cc_start: 0.9427 (tp) cc_final: 0.9114 (tp) REVERT: F 27 GLN cc_start: 0.9006 (mm110) cc_final: 0.8716 (mp10) REVERT: F 46 ILE cc_start: 0.9355 (mt) cc_final: 0.9067 (mt) REVERT: C 56 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7873 (tm-30) REVERT: G 36 LYS cc_start: 0.9194 (mttt) cc_final: 0.8844 (mmmt) REVERT: G 38 ASN cc_start: 0.8839 (m110) cc_final: 0.8424 (m110) REVERT: G 83 LEU cc_start: 0.9316 (mm) cc_final: 0.9111 (mm) REVERT: G 92 GLU cc_start: 0.7776 (tt0) cc_final: 0.7048 (tt0) REVERT: D 36 ILE cc_start: 0.8761 (pt) cc_final: 0.8097 (mm) REVERT: D 38 ILE cc_start: 0.9721 (pt) cc_final: 0.9398 (tt) REVERT: D 43 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8603 (mtpt) REVERT: D 59 MET cc_start: 0.8711 (mmm) cc_final: 0.7522 (mtt) REVERT: D 92 GLN cc_start: 0.8581 (tt0) cc_final: 0.8187 (tm-30) REVERT: H 56 MET cc_start: 0.8387 (tpp) cc_final: 0.8120 (tpp) REVERT: H 64 ASN cc_start: 0.9131 (m-40) cc_final: 0.8270 (t0) REVERT: H 102 GLU cc_start: 0.7945 (tp30) cc_final: 0.7423 (tp30) REVERT: K 256 MSE cc_start: 0.5421 (mtp) cc_final: 0.5029 (mtt) REVERT: K 283 LYS cc_start: 0.3893 (pttm) cc_final: 0.3149 (tptt) REVERT: K 311 MSE cc_start: 0.5732 (mtp) cc_final: 0.5012 (mmm) REVERT: K 314 MSE cc_start: 0.4631 (ttp) cc_final: 0.4054 (ttm) REVERT: K 535 MSE cc_start: 0.6448 (mmm) cc_final: 0.5865 (mmm) REVERT: K 850 MSE cc_start: -0.0389 (tpt) cc_final: -0.0604 (tpp) REVERT: K 872 ARG cc_start: 0.0617 (mmt180) cc_final: -0.0247 (mmt180) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1030 time to fit residues: 37.0512 Evaluate side-chains 199 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** G 110 ASN H 44 GLN ** H 92 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.099273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.071124 restraints weight = 76496.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.070365 restraints weight = 56128.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070700 restraints weight = 47656.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.070858 restraints weight = 39987.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070513 restraints weight = 34949.960| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18226 Z= 0.285 Angle : 0.740 9.949 25843 Z= 0.412 Chirality : 0.042 0.187 2926 Planarity : 0.005 0.062 2271 Dihedral : 29.840 140.251 4754 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.22), residues: 1394 helix: 0.34 (0.18), residues: 802 sheet: -1.93 (0.80), residues: 42 loop : -1.14 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 40 TYR 0.016 0.002 TYR H 37 PHE 0.024 0.002 PHE K 832 TRP 0.010 0.002 TRP K 397 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00633 (18226) covalent geometry : angle 0.73998 (25843) hydrogen bonds : bond 0.07448 ( 837) hydrogen bonds : angle 4.40305 ( 2092) *********************** 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 229 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8789 (mtp) cc_final: 0.8470 (mtp) REVERT: A 125 GLN cc_start: 0.8824 (tp40) cc_final: 0.8511 (tp40) REVERT: E 50 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7760 (mm-30) REVERT: E 54 TYR cc_start: 0.9091 (m-10) cc_final: 0.8793 (m-10) REVERT: E 93 GLN cc_start: 0.8857 (tt0) cc_final: 0.8495 (tm-30) REVERT: E 113 HIS cc_start: 0.8314 (t70) cc_final: 0.8097 (t-170) REVERT: E 120 MET cc_start: 0.9003 (mmm) cc_final: 0.8687 (mmp) REVERT: B 35 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7568 (ttm-80) REVERT: B 46 ILE cc_start: 0.9070 (mt) cc_final: 0.8806 (mm) REVERT: B 79 LYS cc_start: 0.7912 (tppt) cc_final: 0.7700 (tppt) REVERT: B 84 MET cc_start: 0.7975 (tpt) cc_final: 0.7686 (tpp) REVERT: B 92 ARG cc_start: 0.7844 (ptm-80) cc_final: 0.7363 (ttp-170) REVERT: F 46 ILE cc_start: 0.9406 (mt) cc_final: 0.9172 (mt) REVERT: C 56 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7890 (tm-30) REVERT: G 36 LYS cc_start: 0.9250 (mttt) cc_final: 0.8929 (mmmt) REVERT: G 38 ASN cc_start: 0.8942 (m110) cc_final: 0.8539 (m110) REVERT: G 92 GLU cc_start: 0.7967 (tt0) cc_final: 0.7493 (tt0) REVERT: D 38 ILE cc_start: 0.9756 (pt) cc_final: 0.9388 (tt) REVERT: D 43 LYS cc_start: 0.9363 (mmtt) cc_final: 0.8657 (mtpt) REVERT: H 56 MET cc_start: 0.8383 (tpp) cc_final: 0.8118 (tpp) REVERT: H 64 ASN cc_start: 0.9182 (m-40) cc_final: 0.8526 (t0) REVERT: K 256 MSE cc_start: 0.5116 (mtp) cc_final: 0.4797 (mtt) REVERT: K 311 MSE cc_start: 0.5681 (mtp) cc_final: 0.5131 (mmm) REVERT: K 314 MSE cc_start: 0.4214 (ttp) cc_final: 0.3795 (ttm) REVERT: K 535 MSE cc_start: 0.6591 (mmm) cc_final: 0.6071 (mmm) REVERT: K 872 ARG cc_start: 0.0510 (mmt180) cc_final: -0.0388 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1089 time to fit residues: 37.5959 Evaluate side-chains 184 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 115 optimal weight: 30.0000 chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** G 110 ASN H 79 HIS H 92 GLN ** K 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 553 ASN ** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.102144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.072829 restraints weight = 75369.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072016 restraints weight = 51530.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073199 restraints weight = 40638.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073076 restraints weight = 27264.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.073169 restraints weight = 31370.812| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18226 Z= 0.164 Angle : 0.653 8.793 25843 Z= 0.367 Chirality : 0.039 0.154 2926 Planarity : 0.005 0.065 2271 Dihedral : 29.677 135.156 4754 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.08 % Allowed : 0.49 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.23), residues: 1394 helix: 0.56 (0.18), residues: 812 sheet: -2.15 (0.81), residues: 45 loop : -0.97 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 71 TYR 0.019 0.002 TYR C 57 PHE 0.026 0.001 PHE K 832 TRP 0.018 0.002 TRP K 397 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (18226) covalent geometry : angle 0.65255 (25843) hydrogen bonds : bond 0.06905 ( 837) hydrogen bonds : angle 3.96346 ( 2092) ********************** 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 244 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8714 (mtp) cc_final: 0.8337 (mtp) REVERT: A 125 GLN cc_start: 0.8607 (tp40) cc_final: 0.8206 (tp40) REVERT: E 50 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7692 (mm-30) REVERT: E 53 ARG cc_start: 0.8626 (ptm160) cc_final: 0.8337 (ptm160) REVERT: E 93 GLN cc_start: 0.8808 (tt0) cc_final: 0.8519 (tm-30) REVERT: E 113 HIS cc_start: 0.7979 (t70) cc_final: 0.7699 (t-170) REVERT: E 120 MET cc_start: 0.8974 (mmm) cc_final: 0.8621 (mmp) REVERT: B 35 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7563 (ttm-80) REVERT: B 46 ILE cc_start: 0.9059 (mt) cc_final: 0.8802 (mm) REVERT: B 79 LYS cc_start: 0.7890 (tppt) cc_final: 0.7576 (tppt) REVERT: B 84 MET cc_start: 0.7809 (tpt) cc_final: 0.7578 (tpp) REVERT: F 27 GLN cc_start: 0.8945 (mm110) cc_final: 0.8689 (mp10) REVERT: F 46 ILE cc_start: 0.9355 (mt) cc_final: 0.9090 (mt) REVERT: F 63 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 56 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7723 (tm-30) REVERT: G 36 LYS cc_start: 0.9145 (mttt) cc_final: 0.8862 (mmmt) REVERT: G 38 ASN cc_start: 0.8728 (m110) cc_final: 0.8366 (m110) REVERT: G 91 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6575 (tm-30) REVERT: G 92 GLU cc_start: 0.7767 (tt0) cc_final: 0.7392 (mm-30) REVERT: D 36 ILE cc_start: 0.8751 (pt) cc_final: 0.8074 (mm) REVERT: D 38 ILE cc_start: 0.9714 (pt) cc_final: 0.9419 (tt) REVERT: D 43 LYS cc_start: 0.9326 (mmtt) cc_final: 0.8616 (mtpt) REVERT: D 59 MET cc_start: 0.8619 (mmm) cc_final: 0.7758 (mtt) REVERT: H 56 MET cc_start: 0.8391 (tpp) cc_final: 0.8152 (tpp) REVERT: H 64 ASN cc_start: 0.9093 (m-40) cc_final: 0.8601 (t0) REVERT: H 102 GLU cc_start: 0.8020 (tp30) cc_final: 0.7433 (tp30) REVERT: K 247 ARG cc_start: 0.7116 (ttm-80) cc_final: 0.6764 (ptt-90) REVERT: K 256 MSE cc_start: 0.5582 (mtp) cc_final: 0.5212 (mtt) REVERT: K 283 LYS cc_start: 0.4086 (pttm) cc_final: 0.3600 (mmtt) REVERT: K 311 MSE cc_start: 0.5596 (mtp) cc_final: 0.4805 (mmm) REVERT: K 314 MSE cc_start: 0.4224 (ttp) cc_final: 0.3601 (ttm) REVERT: K 535 MSE cc_start: 0.6400 (mmm) cc_final: 0.6001 (mmm) REVERT: K 797 MSE cc_start: 0.0983 (mmt) cc_final: 0.0763 (mmt) REVERT: K 872 ARG cc_start: 0.0450 (mmt180) cc_final: -0.0450 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.1113 time to fit residues: 41.0918 Evaluate side-chains 199 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 9 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 2.1504 ------------------------------------------------------------------------------- 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** G 110 ASN D 92 GLN H 92 GLN ** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.101755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.073239 restraints weight = 76149.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071973 restraints weight = 53163.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072813 restraints weight = 41085.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.072855 restraints weight = 32663.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.072995 restraints weight = 28401.682| |-----------------------------------------------------------------------------| 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 = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5580 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= 0.180 Angle : 0.646 8.933 25843 Z= 0.364 Chirality : 0.038 0.149 2926 Planarity : 0.005 0.065 2271 Dihedral : 29.513 135.724 4754 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1394 helix: 0.66 (0.18), residues: 809 sheet: -2.08 (0.81), residues: 45 loop : -0.89 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 42 TYR 0.013 0.002 TYR H 37 PHE 0.024 0.001 PHE K 832 TRP 0.016 0.001 TRP K 397 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00399 (18226) covalent geometry : angle 0.64636 (25843) hydrogen bonds : bond 0.06867 ( 837) hydrogen bonds : angle 3.89428 ( 2092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2702.13 seconds wall clock time: 47 minutes 26.78 seconds (2846.78 seconds total)