Starting phenix.real_space_refine on Sat Jul 4 05:20:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wha_37537/07_2026/8wha_37537_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wha_37537/07_2026/8wha_37537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wha_37537/07_2026/8wha_37537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wha_37537/07_2026/8wha_37537.map" model { file = "/net/cci-nas-00/data/ceres_data/8wha_37537/07_2026/8wha_37537_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wha_37537/07_2026/8wha_37537_neut.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 288 5.49 5 S 48 5.16 5 Be 2 3.05 5 C 11190 2.51 5 N 3499 2.21 5 O 4051 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19084 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 755 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "B" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 692 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 768 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 688 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 750 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2893 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "J" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2929 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "K" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3669 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 16, 'TRANS': 435} Chain breaks: 1 Chain: "L" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3669 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 16, 'TRANS': 435} Chain breaks: 1 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.09, per 1000 atoms: 0.21 Number of scatterers: 19084 At special positions: 0 Unit cell: (145.35, 170.145, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 48 16.00 P 288 15.00 F 6 9.00 O 4051 8.00 N 3499 7.00 C 11190 6.00 Be 2 4.00 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: 1.32 Conformation dependent library (CDL) restraints added in 481.7 milliseconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3078 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 61.5% alpha, 6.6% beta 108 base pairs and 229 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.182A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.639A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.746A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.696A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.908A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.535A pdb=" N GLY D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.732A pdb=" N ILE D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 149 removed outlier: 3.743A pdb=" N SER D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.606A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.586A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.792A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 removed outlier: 3.803A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.845A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.870A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.689A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.453A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU G 59 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.601A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 removed outlier: 3.786A pdb=" N ASN H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 127 removed outlier: 3.878A pdb=" N THR H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 148 removed outlier: 3.667A pdb=" N ALA H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 220 Processing helix chain 'K' and resid 233 through 246 removed outlier: 6.307A pdb=" N GLY K 239 " --> pdb=" O ILE K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 273 removed outlier: 3.912A pdb=" N SER K 263 " --> pdb=" O LEU K 259 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN K 264 " --> pdb=" O SER K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 291 removed outlier: 3.956A pdb=" N GLU K 290 " --> pdb=" O ASN K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 317 Processing helix chain 'K' and resid 317 through 323 removed outlier: 4.068A pdb=" N ILE K 321 " --> pdb=" O ASP K 317 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG K 323 " --> pdb=" O LYS K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.874A pdb=" N HIS K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU K 352 " --> pdb=" O GLU K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 380 Processing helix chain 'K' and resid 416 through 425 removed outlier: 3.650A pdb=" N ILE K 423 " --> pdb=" O LYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 465 Processing helix chain 'K' and resid 467 through 472 Processing helix chain 'K' and resid 473 through 475 No H-bonds generated for 'chain 'K' and resid 473 through 475' Processing helix chain 'K' and resid 489 through 499 removed outlier: 3.789A pdb=" N ARG K 494 " --> pdb=" O VAL K 490 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS K 495 " --> pdb=" O ILE K 491 " (cutoff:3.500A) Processing helix chain 'K' and resid 500 through 508 removed outlier: 3.796A pdb=" N GLN K 506 " --> pdb=" O LEU K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 519 through 522 Processing helix chain 'K' and resid 523 through 536 Processing helix chain 'K' and resid 550 through 564 removed outlier: 3.564A pdb=" N LYS K 563 " --> pdb=" O TYR K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 575 through 587 Processing helix chain 'K' and resid 599 through 604 Processing helix chain 'K' and resid 623 through 635 removed outlier: 4.112A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN K 629 " --> pdb=" O GLN K 625 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA K 630 " --> pdb=" O MET K 626 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG K 633 " --> pdb=" O GLN K 629 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS K 634 " --> pdb=" O ALA K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 676 removed outlier: 3.559A pdb=" N ARG K 657 " --> pdb=" O SER K 653 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 220 Processing helix chain 'L' and resid 232 through 246 removed outlier: 3.694A pdb=" N GLY L 246 " --> pdb=" O SER L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 273 removed outlier: 3.912A pdb=" N SER L 263 " --> pdb=" O LEU L 259 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN L 264 " --> pdb=" O SER L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 291 removed outlier: 3.956A pdb=" N GLU L 290 " --> pdb=" O ASN L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 Processing helix chain 'L' and resid 317 through 323 removed outlier: 4.067A pdb=" N ILE L 321 " --> pdb=" O ASP L 317 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG L 323 " --> pdb=" O LYS L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 339 Processing helix chain 'L' and resid 343 through 352 removed outlier: 3.874A pdb=" N HIS L 351 " --> pdb=" O ARG L 347 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU L 352 " --> pdb=" O GLU L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 369 through 380 Processing helix chain 'L' and resid 381 through 384 removed outlier: 3.543A pdb=" N PHE L 384 " --> pdb=" O PRO L 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 381 through 384' Processing helix chain 'L' and resid 416 through 425 removed outlier: 3.652A pdb=" N ILE L 423 " --> pdb=" O LYS L 419 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 465 Processing helix chain 'L' and resid 467 through 472 Processing helix chain 'L' and resid 473 through 475 No H-bonds generated for 'chain 'L' and resid 473 through 475' Processing helix chain 'L' and resid 488 through 499 removed outlier: 3.846A pdb=" N ASN L 496 " --> pdb=" O GLN L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 500 through 508 removed outlier: 3.796A pdb=" N GLN L 506 " --> pdb=" O LEU L 502 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE L 507 " --> pdb=" O LEU L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 522 Processing helix chain 'L' and resid 523 through 536 Processing helix chain 'L' and resid 550 through 564 removed outlier: 3.566A pdb=" N LYS L 563 " --> pdb=" O TYR L 559 " (cutoff:3.500A) Processing helix chain 'L' and resid 575 through 587 Processing helix chain 'L' and resid 599 through 604 Processing helix chain 'L' and resid 623 through 635 removed outlier: 4.111A pdb=" N ASP L 627 " --> pdb=" O ASN L 623 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN L 629 " --> pdb=" O GLN L 625 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA L 630 " --> pdb=" O MET L 626 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG L 633 " --> pdb=" O GLN L 629 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS L 634 " --> pdb=" O ALA L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 653 through 676 removed outlier: 3.559A pdb=" N ARG L 657 " --> pdb=" O SER L 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.396A pdb=" N ARG A 83 " --> pdb=" O VAL F 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.266A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.467A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.595A pdb=" N ILE C 79 " --> pdb=" O GLY D 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 7.491A pdb=" N THR F 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.544A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 223 through 225 removed outlier: 4.246A pdb=" N GLY K 223 " --> pdb=" O LYS K 357 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL K 330 " --> pdb=" O LEU K 358 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU K 360 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE K 332 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU K 254 " --> pdb=" O TYR K 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 444 through 450 removed outlier: 6.325A pdb=" N LYS K 444 " --> pdb=" O VAL K 645 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG K 647 " --> pdb=" O LYS K 444 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE K 446 " --> pdb=" O ARG K 647 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER K 649 " --> pdb=" O ILE K 446 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET K 448 " --> pdb=" O SER K 649 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N CYS K 615 " --> pdb=" O TYR K 646 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU K 648 " --> pdb=" O CYS K 615 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU K 617 " --> pdb=" O LEU K 648 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N THR K 650 " --> pdb=" O LEU K 617 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'K' and resid 567 through 570 removed outlier: 6.351A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 223 through 225 removed outlier: 4.246A pdb=" N GLY L 223 " --> pdb=" O LYS L 357 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL L 330 " --> pdb=" O LEU L 358 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU L 360 " --> pdb=" O VAL L 330 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE L 332 " --> pdb=" O LEU L 360 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU L 254 " --> pdb=" O TYR L 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 444 through 450 removed outlier: 6.325A pdb=" N LYS L 444 " --> pdb=" O VAL L 645 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG L 647 " --> pdb=" O LYS L 444 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE L 446 " --> pdb=" O ARG L 647 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER L 649 " --> pdb=" O ILE L 446 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET L 448 " --> pdb=" O SER L 649 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N CYS L 615 " --> pdb=" O TYR L 646 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU L 648 " --> pdb=" O CYS L 615 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU L 617 " --> pdb=" O LEU L 648 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N THR L 650 " --> pdb=" O LEU L 617 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU L 544 " --> pdb=" O ILE L 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 567 through 570 removed outlier: 6.350A pdb=" N CYS L 568 " --> pdb=" O LEU L 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 645 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 269 hydrogen bonds 530 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 229 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2538 1.31 - 1.44: 6620 1.44 - 1.57: 10210 1.57 - 1.70: 582 1.70 - 1.83: 78 Bond restraints: 20028 Sorted by residual: bond pdb=" C1' DT I 134 " pdb=" N1 DT I 134 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.43e+01 bond pdb=" C4 ADP K 802 " pdb=" C5 ADP K 802 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C1' DC I 125 " pdb=" N1 DC I 125 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.97e+01 bond pdb=" C4 ADP L 802 " pdb=" C5 ADP L 802 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C1' DC J 34 " pdb=" N1 DC J 34 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.76e+01 ... (remaining 20023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 27219 3.21 - 6.43: 941 6.43 - 9.64: 73 9.64 - 12.85: 18 12.85 - 16.07: 2 Bond angle restraints: 28253 Sorted by residual: angle pdb=" N THR E 107 " pdb=" CA THR E 107 " pdb=" C THR E 107 " ideal model delta sigma weight residual 113.18 102.18 11.00 1.21e+00 6.83e-01 8.26e+01 angle pdb=" N ARG K 293 " pdb=" CA ARG K 293 " pdb=" C ARG K 293 " ideal model delta sigma weight residual 113.19 102.98 10.21 1.19e+00 7.06e-01 7.36e+01 angle pdb=" N ARG L 293 " pdb=" CA ARG L 293 " pdb=" C ARG L 293 " ideal model delta sigma weight residual 113.19 103.02 10.17 1.19e+00 7.06e-01 7.30e+01 angle pdb=" N HIS G 113 " pdb=" CA HIS G 113 " pdb=" C HIS G 113 " ideal model delta sigma weight residual 108.78 115.18 -6.40 8.20e-01 1.49e+00 6.09e+01 angle pdb=" CA TYR K 513 " pdb=" C TYR K 513 " pdb=" O TYR K 513 " ideal model delta sigma weight residual 120.23 112.38 7.85 1.02e+00 9.61e-01 5.92e+01 ... (remaining 28248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 9936 35.87 - 71.74: 1333 71.74 - 107.61: 36 107.61 - 143.48: 4 143.48 - 179.35: 7 Dihedral angle restraints: 11316 sinusoidal: 6552 harmonic: 4764 Sorted by residual: dihedral pdb=" C5' ADP L 802 " pdb=" O5' ADP L 802 " pdb=" PA ADP L 802 " pdb=" O2A ADP L 802 " ideal model delta sinusoidal sigma weight residual 300.00 155.31 144.70 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" C5' ADP K 802 " pdb=" O5' ADP K 802 " pdb=" PA ADP K 802 " pdb=" O2A ADP K 802 " ideal model delta sinusoidal sigma weight residual 300.00 155.36 144.64 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O2A ADP L 802 " pdb=" O3A ADP L 802 " pdb=" PA ADP L 802 " pdb=" PB ADP L 802 " ideal model delta sinusoidal sigma weight residual -60.00 58.10 -118.10 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 11313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 3123 0.186 - 0.371: 58 0.371 - 0.557: 0 0.557 - 0.742: 1 0.742 - 0.928: 3 Chirality restraints: 3185 Sorted by residual: chirality pdb=" C3' DG I 101 " pdb=" C4' DG I 101 " pdb=" O3' DG I 101 " pdb=" C2' DG I 101 " both_signs ideal model delta sigma weight residual False -2.73 -1.80 -0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" C3' DG I 126 " pdb=" C4' DG I 126 " pdb=" O3' DG I 126 " pdb=" C2' DG I 126 " both_signs ideal model delta sigma weight residual False -2.73 -1.84 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C3' DG J 138 " pdb=" C4' DG J 138 " pdb=" O3' DG J 138 " pdb=" C2' DG J 138 " both_signs ideal model delta sigma weight residual False -2.73 -1.90 -0.83 2.00e-01 2.50e+01 1.71e+01 ... (remaining 3182 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 250 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C ASP K 250 " -0.080 2.00e-02 2.50e+03 pdb=" O ASP K 250 " 0.030 2.00e-02 2.50e+03 pdb=" N GLY K 251 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR K 550 " -0.020 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C THR K 550 " 0.066 2.00e-02 2.50e+03 pdb=" O THR K 550 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS K 551 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 550 " 0.020 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C THR L 550 " -0.065 2.00e-02 2.50e+03 pdb=" O THR L 550 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS L 551 " 0.022 2.00e-02 2.50e+03 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2731 2.75 - 3.29: 18188 3.29 - 3.83: 33616 3.83 - 4.36: 42010 4.36 - 4.90: 61302 Nonbonded interactions: 157847 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.216 3.040 nonbonded pdb=" O ASP C 91 " pdb=" OG SER C 95 " model vdw 2.272 3.040 nonbonded pdb=" NH1 ARG G 30 " pdb=" O THR H 61 " model vdw 2.318 3.120 nonbonded pdb=" OD1 ASN K 368 " pdb=" N SER K 370 " model vdw 2.319 3.120 nonbonded pdb=" OD1 ASN L 368 " pdb=" N SER L 370 " model vdw 2.320 3.120 ... (remaining 157842 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' and resid 41 through 133) } ncs_group { reference = (chain 'B' and resid 17 through 100) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 18 through 116) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 61 through 149) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.970 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.010 0.110 20028 Z= 0.696 Angle : 1.299 16.065 28253 Z= 0.911 Chirality : 0.074 0.928 3185 Planarity : 0.007 0.056 2576 Dihedral : 24.532 179.348 8238 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.51 % Favored : 90.57 % Rotamer: Outliers : 1.40 % Allowed : 6.17 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.19), residues: 1622 helix: -1.34 (0.16), residues: 870 sheet: -2.76 (0.41), residues: 120 loop : -2.81 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 89 TYR 0.041 0.003 TYR L 329 PHE 0.048 0.003 PHE C 26 TRP 0.038 0.002 TRP K 217 HIS 0.014 0.002 HIS K 541 Details of bonding type rmsd/Z covalent geometry : bond 0.01015 / 0.70 (20028) covalent geometry : angle 1.29861 / 0.91 (28253) hydrogen bonds : bond 0.22885 / 15.43 ( 914) hydrogen bonds : angle 9.11710 / 6.38 ( 2423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 541 time to evaluate : 0.587 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 68 GLN cc_start: 0.8716 (tt0) cc_final: 0.8365 (mt0) REVERT: B 25 ASN cc_start: 0.7831 (m-40) cc_final: 0.7488 (m110) REVERT: B 88 TYR cc_start: 0.8317 (m-10) cc_final: 0.7382 (m-10) REVERT: C 25 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8180 (mm-40) REVERT: C 73 ASP cc_start: 0.8119 (t0) cc_final: 0.7809 (t0) REVERT: D 80 SER cc_start: 0.8842 (p) cc_final: 0.8610 (m) REVERT: D 81 SER cc_start: 0.9099 (t) cc_final: 0.8828 (m) REVERT: E 58 THR cc_start: 0.7554 (p) cc_final: 0.7250 (p) REVERT: E 120 MET cc_start: 0.8020 (mpp) cc_final: 0.7776 (mtp) REVERT: E 126 LEU cc_start: 0.9279 (tp) cc_final: 0.9072 (tp) REVERT: F 84 MET cc_start: 0.7503 (tpp) cc_final: 0.7278 (tpp) REVERT: F 88 TYR cc_start: 0.8779 (m-10) cc_final: 0.8005 (m-10) REVERT: F 96 THR cc_start: 0.8856 (m) cc_final: 0.8540 (t) REVERT: G 58 TYR cc_start: 0.7832 (t80) cc_final: 0.7326 (t80) REVERT: K 208 LYS cc_start: 0.8413 (tptt) cc_final: 0.8027 (tttt) REVERT: K 211 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8747 (tptt) REVERT: K 229 MET cc_start: 0.4725 (ptt) cc_final: 0.3369 (ptm) REVERT: K 238 ILE cc_start: 0.6609 (mm) cc_final: 0.5978 (tp) REVERT: K 259 LEU cc_start: 0.7624 (mt) cc_final: 0.7179 (mp) REVERT: K 260 SER cc_start: 0.8420 (p) cc_final: 0.7971 (m) REVERT: K 268 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6201 (mm-30) REVERT: K 269 ILE cc_start: 0.3059 (OUTLIER) cc_final: 0.2565 (mm) REVERT: K 272 PHE cc_start: 0.5472 (m-80) cc_final: 0.5133 (m-80) REVERT: K 312 GLU cc_start: 0.8728 (mp0) cc_final: 0.8403 (mt-10) REVERT: K 313 VAL cc_start: 0.7729 (t) cc_final: 0.7101 (t) REVERT: K 348 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6643 (mt-10) REVERT: K 487 ASN cc_start: 0.7789 (t0) cc_final: 0.7542 (p0) REVERT: K 491 ILE cc_start: 0.8442 (mm) cc_final: 0.8153 (mm) REVERT: K 526 PHE cc_start: 0.7698 (t80) cc_final: 0.7338 (t80) REVERT: K 654 ILE cc_start: 0.8506 (mm) cc_final: 0.8013 (tt) REVERT: L 229 MET cc_start: 0.7645 (ptt) cc_final: 0.7261 (ptm) REVERT: L 261 THR cc_start: 0.8687 (p) cc_final: 0.8347 (t) REVERT: L 268 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8278 (tm-30) REVERT: L 269 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8154 (mt) REVERT: L 279 ILE cc_start: 0.8401 (tp) cc_final: 0.8092 (mt) REVERT: L 322 LEU cc_start: 0.7295 (tp) cc_final: 0.6539 (mt) REVERT: L 359 LEU cc_start: 0.8510 (mt) cc_final: 0.8157 (mp) REVERT: L 379 ILE cc_start: 0.5412 (tp) cc_final: 0.5203 (tp) REVERT: L 442 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7272 (mtm-85) REVERT: L 504 GLN cc_start: 0.8117 (tp40) cc_final: 0.7788 (tp40) REVERT: L 549 TRP cc_start: 0.8417 (m-10) cc_final: 0.7685 (m-10) REVERT: L 628 LEU cc_start: 0.8520 (mt) cc_final: 0.8213 (tp) REVERT: L 660 LYS cc_start: 0.8668 (tttt) cc_final: 0.8441 (mttt) outliers start: 20 outliers final: 0 residues processed: 554 average time/residue: 0.1772 time to fit residues: 136.6567 Evaluate side-chains 270 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 88 ASN D 134 HIS E 55 GLN H 74 HIS ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 282 HIS ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 ASN K 608 ASN ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 341 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.106957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.075154 restraints weight = 71308.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076507 restraints weight = 43955.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.077140 restraints weight = 27453.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.077473 restraints weight = 23062.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077389 restraints weight = 22275.643| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 20028 Z= 0.269 Angle : 0.922 12.471 28253 Z= 0.491 Chirality : 0.055 0.295 3185 Planarity : 0.007 0.095 2576 Dihedral : 28.682 179.082 4914 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.47 % Favored : 93.40 % Rotamer: Outliers : 0.28 % Allowed : 5.33 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.20), residues: 1622 helix: -0.02 (0.16), residues: 924 sheet: -2.29 (0.42), residues: 128 loop : -2.54 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 347 TYR 0.031 0.003 TYR K 558 PHE 0.026 0.002 PHE K 240 TRP 0.046 0.004 TRP L 622 HIS 0.015 0.002 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.27 (20028) covalent geometry : angle 0.92226 / 0.49 (28253) hydrogen bonds : bond 0.08573 / 6.11 ( 914) hydrogen bonds : angle 4.56503 / 3.24 ( 2423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 324 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5702 (mpt180) cc_final: 0.5494 (mpt180) REVERT: A 56 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8341 (mtmm) REVERT: A 59 GLU cc_start: 0.8134 (pp20) cc_final: 0.7504 (pp20) REVERT: A 68 GLN cc_start: 0.8689 (tt0) cc_final: 0.8360 (mt0) REVERT: B 82 THR cc_start: 0.9403 (t) cc_final: 0.9163 (m) REVERT: B 88 TYR cc_start: 0.8746 (m-10) cc_final: 0.8374 (m-80) REVERT: C 25 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8386 (mm-40) REVERT: D 81 SER cc_start: 0.9075 (t) cc_final: 0.8808 (m) REVERT: D 84 MET cc_start: 0.9032 (tpp) cc_final: 0.8764 (tpp) REVERT: D 113 THR cc_start: 0.8792 (m) cc_final: 0.8587 (p) REVERT: E 120 MET cc_start: 0.8338 (mpp) cc_final: 0.8091 (mtp) REVERT: F 84 MET cc_start: 0.8108 (tpp) cc_final: 0.7651 (tpp) REVERT: F 88 TYR cc_start: 0.8884 (m-10) cc_final: 0.8366 (m-10) REVERT: G 57 GLU cc_start: 0.8046 (tt0) cc_final: 0.7751 (mt-10) REVERT: G 58 TYR cc_start: 0.7794 (t80) cc_final: 0.7575 (t80) REVERT: H 98 LEU cc_start: 0.9222 (mt) cc_final: 0.8993 (mp) REVERT: K 229 MET cc_start: 0.3698 (ptt) cc_final: 0.3483 (ptm) REVERT: K 329 TYR cc_start: 0.6040 (m-80) cc_final: 0.5432 (m-80) REVERT: K 506 GLN cc_start: 0.7912 (pt0) cc_final: 0.7702 (pp30) REVERT: K 526 PHE cc_start: 0.7724 (t80) cc_final: 0.7519 (t80) REVERT: K 549 TRP cc_start: 0.7541 (m-10) cc_final: 0.7149 (m-90) REVERT: K 617 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7623 (tp) REVERT: K 654 ILE cc_start: 0.8502 (mm) cc_final: 0.8242 (tt) REVERT: L 229 MET cc_start: 0.7807 (ptt) cc_final: 0.7314 (ptp) REVERT: L 253 TYR cc_start: 0.5149 (t80) cc_final: 0.4879 (t80) REVERT: L 322 LEU cc_start: 0.7667 (tp) cc_final: 0.6863 (mt) REVERT: L 442 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7292 (mtm-85) REVERT: L 452 MET cc_start: 0.6914 (tmm) cc_final: 0.6613 (tmm) REVERT: L 580 ARG cc_start: 0.8729 (ttp80) cc_final: 0.8408 (tmt-80) REVERT: L 660 LYS cc_start: 0.8562 (tttt) cc_final: 0.8344 (mttt) outliers start: 4 outliers final: 0 residues processed: 328 average time/residue: 0.1381 time to fit residues: 66.8724 Evaluate side-chains 234 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 32 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 176 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 150 optimal weight: 0.6980 chunk 107 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 HIS ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 625 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.107357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076096 restraints weight = 71573.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077607 restraints weight = 43409.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.078150 restraints weight = 26534.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078488 restraints weight = 22885.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078502 restraints weight = 21388.596| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20028 Z= 0.165 Angle : 0.700 12.124 28253 Z= 0.388 Chirality : 0.046 0.247 3185 Planarity : 0.005 0.071 2576 Dihedral : 28.475 178.013 4914 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1622 helix: 0.66 (0.17), residues: 935 sheet: -2.01 (0.42), residues: 144 loop : -2.21 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 89 TYR 0.022 0.002 TYR D 108 PHE 0.033 0.002 PHE K 240 TRP 0.022 0.002 TRP L 265 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 (20028) covalent geometry : angle 0.70030 / 0.39 (28253) hydrogen bonds : bond 0.06406 / 4.63 ( 914) hydrogen bonds : angle 4.02177 / 2.87 ( 2423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5562 (mpt180) cc_final: 0.5357 (mpt180) REVERT: A 59 GLU cc_start: 0.8135 (pp20) cc_final: 0.7389 (pp20) REVERT: A 68 GLN cc_start: 0.8686 (tt0) cc_final: 0.8411 (mt0) REVERT: B 88 TYR cc_start: 0.8655 (m-10) cc_final: 0.8162 (m-10) REVERT: C 25 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8391 (mm-40) REVERT: C 73 ASP cc_start: 0.8302 (t0) cc_final: 0.8063 (t0) REVERT: D 84 MET cc_start: 0.8908 (tpp) cc_final: 0.8508 (tpp) REVERT: D 113 THR cc_start: 0.8729 (m) cc_final: 0.8518 (p) REVERT: E 120 MET cc_start: 0.8329 (mpp) cc_final: 0.8115 (mtp) REVERT: G 57 GLU cc_start: 0.8057 (tt0) cc_final: 0.7723 (mt-10) REVERT: G 62 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7068 (mt-10) REVERT: H 76 ASP cc_start: 0.8283 (p0) cc_final: 0.7960 (p0) REVERT: H 98 LEU cc_start: 0.9239 (mt) cc_final: 0.8995 (mp) REVERT: H 120 GLN cc_start: 0.8557 (mm110) cc_final: 0.8342 (tp40) REVERT: K 348 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6986 (mm-30) REVERT: K 491 ILE cc_start: 0.8298 (mm) cc_final: 0.8045 (mp) REVERT: K 506 GLN cc_start: 0.7796 (pt0) cc_final: 0.7585 (pp30) REVERT: K 549 TRP cc_start: 0.7578 (m-10) cc_final: 0.7242 (m-90) REVERT: K 559 TYR cc_start: 0.4478 (t80) cc_final: 0.4234 (t80) REVERT: K 616 ILE cc_start: 0.7359 (tp) cc_final: 0.7046 (tp) REVERT: K 654 ILE cc_start: 0.8572 (mm) cc_final: 0.8372 (tt) REVERT: L 315 MET cc_start: 0.8318 (ttm) cc_final: 0.7501 (mtm) REVERT: L 322 LEU cc_start: 0.7722 (tp) cc_final: 0.6952 (mt) REVERT: L 428 ILE cc_start: 0.7850 (mp) cc_final: 0.7645 (mp) REVERT: L 442 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7299 (mtm-85) REVERT: L 452 MET cc_start: 0.6895 (tmm) cc_final: 0.6580 (tmm) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1479 time to fit residues: 70.9226 Evaluate side-chains 212 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 137 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 625 GLN ** K 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.104568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073007 restraints weight = 71402.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074264 restraints weight = 43434.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074825 restraints weight = 27508.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.075136 restraints weight = 23280.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.075113 restraints weight = 22375.205| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20028 Z= 0.185 Angle : 0.705 12.263 28253 Z= 0.386 Chirality : 0.045 0.222 3185 Planarity : 0.005 0.066 2576 Dihedral : 28.384 178.713 4914 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.17 % Favored : 93.77 % Rotamer: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1622 helix: 1.00 (0.17), residues: 938 sheet: -1.77 (0.46), residues: 124 loop : -1.98 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 89 TYR 0.017 0.002 TYR H 108 PHE 0.030 0.002 PHE K 240 TRP 0.018 0.002 TRP K 217 HIS 0.005 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (20028) covalent geometry : angle 0.70531 / 0.39 (28253) hydrogen bonds : bond 0.06336 / 4.57 ( 914) hydrogen bonds : angle 3.87371 / 2.77 ( 2423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5672 (mpt180) cc_final: 0.5347 (mpt180) REVERT: A 59 GLU cc_start: 0.7888 (pp20) cc_final: 0.7414 (pp20) REVERT: A 68 GLN cc_start: 0.8725 (tt0) cc_final: 0.8462 (mt0) REVERT: C 25 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8320 (mm-40) REVERT: D 84 MET cc_start: 0.8899 (tpp) cc_final: 0.8527 (tpp) REVERT: E 120 MET cc_start: 0.8426 (mpp) cc_final: 0.7974 (mtp) REVERT: F 88 TYR cc_start: 0.8811 (m-10) cc_final: 0.8431 (m-10) REVERT: G 57 GLU cc_start: 0.8141 (tt0) cc_final: 0.7799 (mt-10) REVERT: G 58 TYR cc_start: 0.7742 (t80) cc_final: 0.7190 (t80) REVERT: G 62 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6964 (mt-10) REVERT: K 260 SER cc_start: 0.8366 (m) cc_final: 0.8141 (m) REVERT: K 469 GLU cc_start: 0.7109 (pt0) cc_final: 0.6758 (tp30) REVERT: K 491 ILE cc_start: 0.8252 (mm) cc_final: 0.8014 (mp) REVERT: K 506 GLN cc_start: 0.7740 (pt0) cc_final: 0.7489 (pp30) REVERT: K 549 TRP cc_start: 0.7673 (m-10) cc_final: 0.7246 (m-90) REVERT: L 229 MET cc_start: 0.7364 (ptp) cc_final: 0.6295 (ptp) REVERT: L 315 MET cc_start: 0.8450 (ttm) cc_final: 0.7518 (mtm) REVERT: L 352 LEU cc_start: 0.6961 (mm) cc_final: 0.6696 (mm) REVERT: L 354 MET cc_start: 0.7655 (mpp) cc_final: 0.7420 (mpp) REVERT: L 442 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7291 (mtm-85) REVERT: L 452 MET cc_start: 0.6989 (tmm) cc_final: 0.6720 (tmm) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.1348 time to fit residues: 56.3616 Evaluate side-chains 202 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 90 optimal weight: 30.0000 chunk 184 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 ASN ** K 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 341 HIS L 462 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.102270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.070311 restraints weight = 71736.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071712 restraints weight = 42994.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072626 restraints weight = 26676.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072638 restraints weight = 23351.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072596 restraints weight = 22025.245| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20028 Z= 0.205 Angle : 0.718 12.968 28253 Z= 0.392 Chirality : 0.046 0.279 3185 Planarity : 0.005 0.059 2576 Dihedral : 28.274 177.497 4914 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1622 helix: 1.17 (0.17), residues: 936 sheet: -1.94 (0.43), residues: 132 loop : -1.78 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 83 TYR 0.014 0.002 TYR K 311 PHE 0.034 0.002 PHE K 240 TRP 0.022 0.002 TRP K 327 HIS 0.011 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (20028) covalent geometry : angle 0.71764 / 0.39 (28253) hydrogen bonds : bond 0.06347 / 4.54 ( 914) hydrogen bonds : angle 3.85027 / 2.75 ( 2423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5555 (mpt180) cc_final: 0.5119 (mpt180) REVERT: A 59 GLU cc_start: 0.7930 (pp20) cc_final: 0.7466 (pp20) REVERT: A 68 GLN cc_start: 0.8736 (tt0) cc_final: 0.8455 (mt0) REVERT: C 65 GLU cc_start: 0.8516 (pt0) cc_final: 0.8110 (pt0) REVERT: E 120 MET cc_start: 0.8633 (mpp) cc_final: 0.8351 (mtp) REVERT: G 57 GLU cc_start: 0.8165 (tt0) cc_final: 0.7959 (tt0) REVERT: H 76 ASP cc_start: 0.8213 (p0) cc_final: 0.7978 (p0) REVERT: H 110 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8170 (mmmm) REVERT: K 280 ILE cc_start: 0.6859 (mt) cc_final: 0.6616 (mp) REVERT: K 469 GLU cc_start: 0.7226 (pt0) cc_final: 0.6786 (tp30) REVERT: K 506 GLN cc_start: 0.7720 (pt0) cc_final: 0.7430 (pp30) REVERT: K 559 TYR cc_start: 0.4767 (t80) cc_final: 0.3989 (t80) REVERT: K 577 ASP cc_start: 0.7856 (t0) cc_final: 0.7395 (p0) REVERT: L 206 GLN cc_start: 0.8078 (mt0) cc_final: 0.7626 (tm-30) REVERT: L 229 MET cc_start: 0.7350 (ptp) cc_final: 0.6106 (ptp) REVERT: L 315 MET cc_start: 0.8498 (ttm) cc_final: 0.7578 (mtm) REVERT: L 322 LEU cc_start: 0.7984 (tp) cc_final: 0.7430 (pp) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.1366 time to fit residues: 57.3583 Evaluate side-chains 194 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 181 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 157 optimal weight: 0.0970 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 HIS ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.103070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070468 restraints weight = 70565.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.072150 restraints weight = 39014.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073138 restraints weight = 27556.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073659 restraints weight = 22967.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073908 restraints weight = 20866.454| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20028 Z= 0.152 Angle : 0.670 10.943 28253 Z= 0.369 Chirality : 0.044 0.227 3185 Planarity : 0.004 0.050 2576 Dihedral : 28.165 178.063 4914 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.21), residues: 1622 helix: 1.33 (0.17), residues: 933 sheet: -1.86 (0.41), residues: 150 loop : -1.78 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.031 0.002 TYR D 108 PHE 0.024 0.001 PHE K 240 TRP 0.019 0.002 TRP K 217 HIS 0.006 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (20028) covalent geometry : angle 0.67030 / 0.37 (28253) hydrogen bonds : bond 0.05708 / 4.15 ( 914) hydrogen bonds : angle 3.64407 / 2.60 ( 2423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8539 (m) cc_final: 0.8171 (p) REVERT: A 59 GLU cc_start: 0.7923 (pp20) cc_final: 0.7390 (pp20) REVERT: A 64 LYS cc_start: 0.9021 (mptt) cc_final: 0.8569 (mmtp) REVERT: A 68 GLN cc_start: 0.8671 (tt0) cc_final: 0.8464 (mt0) REVERT: B 88 TYR cc_start: 0.8596 (m-80) cc_final: 0.8225 (m-80) REVERT: C 65 GLU cc_start: 0.8539 (pt0) cc_final: 0.7952 (pt0) REVERT: D 72 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8408 (tm-30) REVERT: E 120 MET cc_start: 0.8692 (mpp) cc_final: 0.8298 (mtp) REVERT: G 57 GLU cc_start: 0.8188 (tt0) cc_final: 0.7950 (tt0) REVERT: H 111 LYS cc_start: 0.8886 (mptt) cc_final: 0.8675 (mmtm) REVERT: K 280 ILE cc_start: 0.6937 (mt) cc_final: 0.6711 (mp) REVERT: K 363 THR cc_start: 0.7778 (m) cc_final: 0.7315 (m) REVERT: K 469 GLU cc_start: 0.7297 (pt0) cc_final: 0.6881 (tp30) REVERT: K 506 GLN cc_start: 0.7712 (pt0) cc_final: 0.7449 (pp30) REVERT: K 549 TRP cc_start: 0.7978 (m-10) cc_final: 0.7429 (m-90) REVERT: K 577 ASP cc_start: 0.7959 (t0) cc_final: 0.7511 (p0) REVERT: K 661 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8113 (ttp80) REVERT: L 206 GLN cc_start: 0.8020 (mt0) cc_final: 0.7641 (tm-30) REVERT: L 229 MET cc_start: 0.7518 (ptp) cc_final: 0.6356 (ptp) REVERT: L 322 LEU cc_start: 0.8002 (tp) cc_final: 0.7633 (pp) REVERT: L 352 LEU cc_start: 0.7083 (mm) cc_final: 0.6802 (mm) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1249 time to fit residues: 52.2513 Evaluate side-chains 197 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 47 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 136 optimal weight: 0.0070 chunk 88 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 72 optimal weight: 30.0000 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 HIS D 88 ASN D 92 ASN E 93 GLN G 105 ASN ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 608 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.102705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070084 restraints weight = 70863.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071809 restraints weight = 38067.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072794 restraints weight = 26610.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073340 restraints weight = 21988.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073572 restraints weight = 19978.545| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20028 Z= 0.149 Angle : 0.662 11.244 28253 Z= 0.363 Chirality : 0.044 0.238 3185 Planarity : 0.004 0.040 2576 Dihedral : 28.088 177.771 4914 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z 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 (0.21), residues: 1622 helix: 1.41 (0.17), residues: 946 sheet: -1.77 (0.42), residues: 150 loop : -1.89 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 19 TYR 0.019 0.002 TYR K 513 PHE 0.025 0.001 PHE K 240 TRP 0.023 0.002 TRP K 373 HIS 0.007 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (20028) covalent geometry : angle 0.66157 / 0.36 (28253) hydrogen bonds : bond 0.05611 / 4.10 ( 914) hydrogen bonds : angle 3.57858 / 2.55 ( 2423) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8611 (m) cc_final: 0.8256 (p) REVERT: A 59 GLU cc_start: 0.7786 (pp20) cc_final: 0.7316 (pp20) REVERT: A 64 LYS cc_start: 0.9014 (mptt) cc_final: 0.8632 (mmtp) REVERT: B 84 MET cc_start: 0.8447 (mmm) cc_final: 0.8163 (mmm) REVERT: C 62 GLU cc_start: 0.7902 (tp30) cc_final: 0.7586 (tp30) REVERT: C 65 GLU cc_start: 0.8553 (pt0) cc_final: 0.7854 (pt0) REVERT: C 96 LYS cc_start: 0.8633 (mppt) cc_final: 0.7860 (mtmm) REVERT: D 72 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8442 (tm-30) REVERT: E 120 MET cc_start: 0.8718 (mpp) cc_final: 0.8311 (mtp) REVERT: G 57 GLU cc_start: 0.8182 (tt0) cc_final: 0.7966 (tt0) REVERT: H 111 LYS cc_start: 0.8951 (mptt) cc_final: 0.8724 (mmtm) REVERT: K 363 THR cc_start: 0.7813 (m) cc_final: 0.7370 (m) REVERT: K 469 GLU cc_start: 0.7271 (pt0) cc_final: 0.6829 (tp30) REVERT: K 506 GLN cc_start: 0.7675 (pt0) cc_final: 0.7374 (pp30) REVERT: K 549 TRP cc_start: 0.8022 (m-10) cc_final: 0.7476 (m-90) REVERT: K 577 ASP cc_start: 0.7953 (t0) cc_final: 0.7483 (p0) REVERT: L 206 GLN cc_start: 0.8017 (mt0) cc_final: 0.7645 (tm-30) REVERT: L 229 MET cc_start: 0.7521 (ptp) cc_final: 0.6413 (ptp) REVERT: L 315 MET cc_start: 0.8396 (ttm) cc_final: 0.7834 (mtm) REVERT: L 322 LEU cc_start: 0.8012 (tp) cc_final: 0.7647 (pp) REVERT: L 446 ILE cc_start: 0.7638 (mp) cc_final: 0.7225 (tp) REVERT: L 598 LEU cc_start: 0.7605 (tt) cc_final: 0.7033 (tt) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1332 time to fit residues: 54.4579 Evaluate side-chains 190 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 167 optimal weight: 0.0070 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 74 HIS ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.101860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.068836 restraints weight = 71693.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070485 restraints weight = 40012.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071432 restraints weight = 28548.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071932 restraints weight = 23837.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072204 restraints weight = 21844.335| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20028 Z= 0.173 Angle : 0.683 11.766 28253 Z= 0.373 Chirality : 0.044 0.251 3185 Planarity : 0.004 0.041 2576 Dihedral : 28.029 177.368 4914 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z 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: 0.12 (0.21), residues: 1622 helix: 1.45 (0.17), residues: 946 sheet: -1.81 (0.42), residues: 152 loop : -1.88 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 636 TYR 0.019 0.002 TYR K 559 PHE 0.021 0.002 PHE K 240 TRP 0.070 0.002 TRP K 265 HIS 0.008 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (20028) covalent geometry : angle 0.68277 / 0.37 (28253) hydrogen bonds : bond 0.05829 / 4.22 ( 914) hydrogen bonds : angle 3.65085 / 2.59 ( 2423) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8659 (m) cc_final: 0.8309 (p) REVERT: A 59 GLU cc_start: 0.7784 (pp20) cc_final: 0.7332 (pp20) REVERT: B 84 MET cc_start: 0.8473 (mmm) cc_final: 0.8203 (mmm) REVERT: B 88 TYR cc_start: 0.8382 (m-80) cc_final: 0.7804 (m-80) REVERT: C 62 GLU cc_start: 0.7757 (tp30) cc_final: 0.7262 (tp30) REVERT: C 65 GLU cc_start: 0.8462 (pt0) cc_final: 0.7741 (pt0) REVERT: C 96 LYS cc_start: 0.8600 (mppt) cc_final: 0.8052 (mmtp) REVERT: D 72 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8458 (tm-30) REVERT: E 120 MET cc_start: 0.8754 (mpp) cc_final: 0.8350 (mtp) REVERT: F 50 ILE cc_start: 0.9459 (mm) cc_final: 0.9252 (mm) REVERT: G 57 GLU cc_start: 0.8177 (tt0) cc_final: 0.7972 (tt0) REVERT: G 58 TYR cc_start: 0.8183 (t80) cc_final: 0.7954 (t80) REVERT: H 111 LYS cc_start: 0.8996 (mptt) cc_final: 0.8777 (mmtm) REVERT: K 432 MET cc_start: 0.4853 (mpp) cc_final: 0.4511 (ptp) REVERT: K 469 GLU cc_start: 0.7286 (pt0) cc_final: 0.6801 (tp30) REVERT: K 506 GLN cc_start: 0.7683 (pt0) cc_final: 0.7362 (pp30) REVERT: K 577 ASP cc_start: 0.8109 (t0) cc_final: 0.7674 (p0) REVERT: L 206 GLN cc_start: 0.8040 (mt0) cc_final: 0.7663 (tm-30) REVERT: L 229 MET cc_start: 0.7549 (ptp) cc_final: 0.6508 (ptp) REVERT: L 315 MET cc_start: 0.8451 (ttm) cc_final: 0.7863 (mtm) REVERT: L 446 ILE cc_start: 0.7627 (mp) cc_final: 0.7222 (tp) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1322 time to fit residues: 50.8445 Evaluate side-chains 182 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 16 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 83 optimal weight: 40.0000 chunk 174 optimal weight: 3.9990 chunk 159 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.101068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070098 restraints weight = 70656.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.071084 restraints weight = 42037.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.071591 restraints weight = 28723.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071911 restraints weight = 24166.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071826 restraints weight = 22759.077| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20028 Z= 0.166 Angle : 0.678 12.151 28253 Z= 0.370 Chirality : 0.044 0.277 3185 Planarity : 0.004 0.045 2576 Dihedral : 27.961 177.176 4914 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1622 helix: 1.44 (0.17), residues: 946 sheet: -1.23 (0.48), residues: 124 loop : -1.91 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 580 TYR 0.042 0.002 TYR H 108 PHE 0.020 0.001 PHE K 240 TRP 0.058 0.002 TRP K 265 HIS 0.007 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (20028) covalent geometry : angle 0.67844 / 0.37 (28253) hydrogen bonds : bond 0.05690 / 4.14 ( 914) hydrogen bonds : angle 3.61490 / 2.57 ( 2423) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7827 (pp20) cc_final: 0.7319 (pp20) REVERT: B 84 MET cc_start: 0.8431 (mmm) cc_final: 0.8158 (mmm) REVERT: C 62 GLU cc_start: 0.7695 (tp30) cc_final: 0.7234 (tp30) REVERT: C 65 GLU cc_start: 0.8441 (pt0) cc_final: 0.7751 (pt0) REVERT: C 96 LYS cc_start: 0.8352 (mppt) cc_final: 0.7885 (mmtp) REVERT: E 56 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8787 (tptt) REVERT: E 120 MET cc_start: 0.8755 (mpp) cc_final: 0.8382 (mtp) REVERT: F 50 ILE cc_start: 0.9445 (mm) cc_final: 0.9228 (mm) REVERT: G 57 GLU cc_start: 0.8196 (tt0) cc_final: 0.7982 (tt0) REVERT: H 111 LYS cc_start: 0.8952 (mptt) cc_final: 0.8724 (mmtm) REVERT: K 469 GLU cc_start: 0.7373 (pt0) cc_final: 0.6835 (tp30) REVERT: K 506 GLN cc_start: 0.7769 (pt0) cc_final: 0.7408 (pp30) REVERT: K 577 ASP cc_start: 0.7904 (t0) cc_final: 0.7583 (p0) REVERT: L 206 GLN cc_start: 0.8121 (mt0) cc_final: 0.7760 (tm-30) REVERT: L 229 MET cc_start: 0.7407 (ptp) cc_final: 0.6470 (ptp) REVERT: L 315 MET cc_start: 0.8450 (ttm) cc_final: 0.7911 (mtm) REVERT: L 446 ILE cc_start: 0.7610 (mp) cc_final: 0.7098 (tp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1260 time to fit residues: 46.2705 Evaluate side-chains 180 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 23 optimal weight: 2.9990 chunk 171 optimal weight: 0.0670 chunk 157 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 81 optimal weight: 40.0000 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068486 restraints weight = 70976.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070190 restraints weight = 38461.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.071187 restraints weight = 26920.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.071680 restraints weight = 22267.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072031 restraints weight = 20299.848| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20028 Z= 0.142 Angle : 0.660 12.066 28253 Z= 0.360 Chirality : 0.043 0.306 3185 Planarity : 0.004 0.045 2576 Dihedral : 27.920 177.494 4914 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1622 helix: 1.53 (0.17), residues: 947 sheet: -1.17 (0.48), residues: 124 loop : -1.89 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 107 TYR 0.019 0.002 TYR K 559 PHE 0.022 0.001 PHE K 240 TRP 0.064 0.002 TRP K 265 HIS 0.005 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (20028) covalent geometry : angle 0.65957 / 0.36 (28253) hydrogen bonds : bond 0.05451 / 4.00 ( 914) hydrogen bonds : angle 3.53228 / 2.51 ( 2423) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8590 (m) cc_final: 0.8264 (p) REVERT: A 59 GLU cc_start: 0.7747 (pp20) cc_final: 0.7375 (pp20) REVERT: C 62 GLU cc_start: 0.7682 (tp30) cc_final: 0.7221 (tp30) REVERT: C 65 GLU cc_start: 0.8399 (pt0) cc_final: 0.7801 (pt0) REVERT: C 96 LYS cc_start: 0.8316 (mppt) cc_final: 0.7915 (mmtp) REVERT: E 56 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8807 (tptt) REVERT: E 120 MET cc_start: 0.8730 (mpp) cc_final: 0.8376 (mtp) REVERT: F 50 ILE cc_start: 0.9370 (mm) cc_final: 0.9162 (mm) REVERT: F 88 TYR cc_start: 0.8619 (m-10) cc_final: 0.8222 (m-10) REVERT: G 57 GLU cc_start: 0.8160 (tt0) cc_final: 0.7939 (tt0) REVERT: H 111 LYS cc_start: 0.8975 (mptt) cc_final: 0.8763 (mmtm) REVERT: K 292 ARG cc_start: 0.7225 (mpp-170) cc_final: 0.6708 (mmm160) REVERT: K 373 TRP cc_start: 0.6882 (t60) cc_final: 0.6639 (t60) REVERT: K 469 GLU cc_start: 0.7403 (pt0) cc_final: 0.6864 (tp30) REVERT: K 506 GLN cc_start: 0.7683 (pt0) cc_final: 0.7341 (pp30) REVERT: K 577 ASP cc_start: 0.7872 (t0) cc_final: 0.7548 (p0) REVERT: L 229 MET cc_start: 0.7533 (ptp) cc_final: 0.6627 (ptp) REVERT: L 315 MET cc_start: 0.8466 (ttm) cc_final: 0.7963 (mtm) REVERT: L 432 MET cc_start: 0.6589 (mmm) cc_final: 0.6337 (tpp) REVERT: L 446 ILE cc_start: 0.7562 (mp) cc_final: 0.7140 (tp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1278 time to fit residues: 48.0666 Evaluate side-chains 186 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 71 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 90 optimal weight: 30.0000 chunk 120 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.100205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067337 restraints weight = 71473.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068995 restraints weight = 39018.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070008 restraints weight = 27360.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070548 restraints weight = 22576.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070815 restraints weight = 20463.832| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20028 Z= 0.176 Angle : 0.693 11.429 28253 Z= 0.377 Chirality : 0.044 0.317 3185 Planarity : 0.004 0.046 2576 Dihedral : 27.945 177.126 4914 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1622 helix: 1.38 (0.17), residues: 959 sheet: -1.42 (0.48), residues: 112 loop : -1.79 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 636 TYR 0.025 0.002 TYR K 559 PHE 0.018 0.001 PHE K 240 TRP 0.064 0.002 TRP K 265 HIS 0.007 0.001 HIS K 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (20028) covalent geometry : angle 0.69339 / 0.38 (28253) hydrogen bonds : bond 0.05810 / 4.21 ( 914) hydrogen bonds : angle 3.64535 / 2.59 ( 2423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.25 seconds wall clock time: 57 minutes 1.61 seconds (3421.61 seconds total)