Starting phenix.real_space_refine on Sun Aug 24 09:03:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wha_37537/08_2025/8wha_37537_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wha_37537/08_2025/8wha_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_37537/08_2025/8wha_37537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wha_37537/08_2025/8wha_37537.map" model { file = "/net/cci-nas-00/data/ceres_data/8wha_37537/08_2025/8wha_37537_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wha_37537/08_2025/8wha_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-2.0-5787/lib/python3.9/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: 4.93, per 1000 atoms: 0.26 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: 1.84 Conformation dependent library (CDL) restraints added in 697.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.83 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: 4.24 Time building geometry restraints manager: 2.45 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=" 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=" 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=" F1 BEF L 801 " pdb="BE BEF L 801 " ideal model delta sigma weight residual 1.476 1.575 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" F1 BEF K 801 " pdb="BE BEF K 801 " ideal model delta sigma weight residual 1.476 1.573 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" N TYR L 513 " pdb=" CA TYR L 513 " ideal model delta sigma weight residual 1.457 1.521 -0.064 1.41e-02 5.03e+03 2.09e+01 ... (remaining 20023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 26824 2.79 - 5.59: 1282 5.59 - 8.38: 111 8.38 - 11.17: 27 11.17 - 13.97: 9 Bond angle restraints: 28253 Sorted by residual: angle pdb=" O3' DT J 9 " pdb=" C3' DT J 9 " pdb=" C2' DT J 9 " ideal model delta sigma weight residual 111.50 125.47 -13.97 1.50e+00 4.44e-01 8.67e+01 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=" O3' DG I 126 " pdb=" C3' DG I 126 " pdb=" C2' DG I 126 " ideal model delta sigma weight residual 111.50 124.55 -13.05 1.50e+00 4.44e-01 7.56e+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 ... (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 - 0.171: 3095 0.171 - 0.343: 86 0.343 - 0.514: 0 0.514 - 0.686: 1 0.686 - 0.857: 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 -2.66 -1.80 -0.86 2.00e-01 2.50e+01 1.84e+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 -2.66 -1.84 -0.82 2.00e-01 2.50e+01 1.70e+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 -2.66 -1.90 -0.76 2.00e-01 2.50e+01 1.43e+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: 1.130 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.900 Find NCS groups from input model: 0.170 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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= 0.625 Angle : 1.295 13.965 28253 Z= 0.873 Chirality : 0.070 0.857 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 aren 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 covalent geometry : bond 0.01006 (20028) covalent geometry : angle 1.29474 (28253) hydrogen bonds : bond 0.22885 ( 914) hydrogen bonds : angle 9.11710 ( 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 : 0.613 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: 0.8715 (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: 0.8630 (mm-40) cc_final: 0.8180 (mm-40) REVERT: C 73 ASP cc_start: 0.8120 (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: 0.7505 (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: 0.7279 (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: 0.2113 time to fit residues: 160.5813 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 : 0.533 ------------------------------------------------------------------------------- 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: 8.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 ASN E 55 GLN H 74 HIS ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 282 HIS ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 HIS ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 ASN K 608 ASN ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 ASN ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 608 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.103635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.071662 restraints weight = 70333.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072992 restraints weight = 43358.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.073499 restraints weight = 27429.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073851 restraints weight = 23107.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073716 restraints weight = 22179.549| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 20028 Z= 0.283 Angle : 0.820 10.674 28253 Z= 0.444 Chirality : 0.046 0.231 3185 Planarity : 0.006 0.056 2576 Dihedral : 28.398 179.959 4914 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.28 % Rotamer: Outliers : 0.14 % Allowed : 4.84 % Favored : 95.02 % 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 aren not related in a simple way. whole: -1.33 (0.20), residues: 1622 helix: 0.25 (0.17), residues: 923 sheet: -2.36 (0.42), residues: 132 loop : -2.36 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 19 TYR 0.027 0.002 TYR D 108 PHE 0.031 0.003 PHE K 240 TRP 0.027 0.003 TRP L 622 HIS 0.007 0.002 HIS K 455 Details of bonding type rmsd covalent geometry : bond 0.00645 (20028) covalent geometry : angle 0.82044 (28253) hydrogen bonds : bond 0.07286 ( 914) hydrogen bonds : angle 4.32550 ( 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 331 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 329 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5608 (mpt180) cc_final: 0.5312 (mpt180) REVERT: A 46 VAL cc_start: 0.8558 (m) cc_final: 0.8248 (p) REVERT: A 59 GLU cc_start: 0.8097 (pp20) cc_final: 0.7429 (pp20) REVERT: A 68 GLN cc_start: 0.8715 (tt0) cc_final: 0.8424 (mt0) REVERT: A 77 ASP cc_start: 0.8615 (p0) cc_final: 0.8360 (p0) REVERT: A 107 THR cc_start: 0.9525 (m) cc_final: 0.9248 (t) REVERT: C 25 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8370 (mm-40) REVERT: D 81 SER cc_start: 0.9030 (t) cc_final: 0.8743 (m) REVERT: E 120 MET cc_start: 0.8556 (mpp) cc_final: 0.8310 (mtp) REVERT: H 76 ASP cc_start: 0.8348 (p0) cc_final: 0.8124 (p0) REVERT: K 229 MET cc_start: 0.4330 (ptt) cc_final: 0.3827 (ptt) REVERT: K 241 LEU cc_start: 0.6370 (mm) cc_final: 0.6061 (pp) REVERT: K 259 LEU cc_start: 0.7870 (mt) cc_final: 0.7643 (mp) REVERT: K 312 GLU cc_start: 0.8605 (mp0) cc_final: 0.8276 (mt-10) REVERT: K 329 TYR cc_start: 0.6099 (m-80) cc_final: 0.5504 (m-80) REVERT: K 348 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6975 (mm-30) REVERT: K 487 ASN cc_start: 0.7842 (t0) cc_final: 0.7392 (p0) REVERT: K 549 TRP cc_start: 0.7727 (m-10) cc_final: 0.7427 (m-90) REVERT: K 559 TYR cc_start: 0.4649 (t80) cc_final: 0.4344 (t80) REVERT: K 617 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7067 (tp) REVERT: L 268 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7966 (tm-30) REVERT: L 315 MET cc_start: 0.8392 (ttt) cc_final: 0.8155 (ttm) REVERT: L 442 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7316 (mtm-85) REVERT: L 580 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8615 (tmt-80) REVERT: L 660 LYS cc_start: 0.8428 (tttt) cc_final: 0.8193 (mttt) REVERT: L 669 GLU cc_start: 0.7478 (pp20) cc_final: 0.7164 (tm-30) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.1699 time to fit residues: 81.6897 Evaluate side-chains 213 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 176 optimal weight: 9.9990 chunk 112 optimal weight: 0.3980 chunk 92 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 267 ASN ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 ASN L 236 GLN L 264 ASN L 496 ASN L 625 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.105044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.072352 restraints weight = 71353.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.074198 restraints weight = 37617.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075301 restraints weight = 25919.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075890 restraints weight = 21252.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076157 restraints weight = 19217.258| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20028 Z= 0.148 Angle : 0.641 10.966 28253 Z= 0.352 Chirality : 0.038 0.163 3185 Planarity : 0.004 0.045 2576 Dihedral : 28.013 178.400 4914 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.51 % Rotamer: Outliers : 0.14 % Allowed : 3.43 % Favored : 96.43 % 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 aren not related in a simple way. whole: -0.39 (0.21), residues: 1622 helix: 1.08 (0.17), residues: 933 sheet: -2.05 (0.41), residues: 144 loop : -2.13 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 636 TYR 0.029 0.002 TYR D 108 PHE 0.026 0.001 PHE K 240 TRP 0.022 0.002 TRP L 265 HIS 0.006 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00314 (20028) covalent geometry : angle 0.64118 (28253) hydrogen bonds : bond 0.05402 ( 914) hydrogen bonds : angle 3.67413 ( 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 319 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5497 (mpt180) cc_final: 0.5170 (mpt180) REVERT: A 59 GLU cc_start: 0.8137 (pp20) cc_final: 0.7414 (pp20) REVERT: A 64 LYS cc_start: 0.9066 (mptt) cc_final: 0.8578 (mmtp) REVERT: A 107 THR cc_start: 0.9443 (m) cc_final: 0.9123 (t) REVERT: B 82 THR cc_start: 0.9235 (t) cc_final: 0.9014 (m) REVERT: C 65 GLU cc_start: 0.8455 (pt0) cc_final: 0.7602 (pt0) REVERT: C 91 ASP cc_start: 0.8289 (t0) cc_final: 0.8028 (t0) REVERT: D 84 MET cc_start: 0.8797 (tpp) cc_final: 0.8197 (tpp) REVERT: E 120 MET cc_start: 0.8592 (mpp) cc_final: 0.8192 (mtp) REVERT: G 62 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7233 (mt-10) REVERT: H 76 ASP cc_start: 0.8186 (p0) cc_final: 0.7903 (p0) REVERT: K 241 LEU cc_start: 0.6561 (mm) cc_final: 0.6334 (pp) REVERT: K 329 TYR cc_start: 0.6092 (m-80) cc_final: 0.5324 (m-80) REVERT: K 384 PHE cc_start: 0.6962 (m-10) cc_final: 0.6701 (m-10) REVERT: K 469 GLU cc_start: 0.7230 (pt0) cc_final: 0.6951 (tp30) REVERT: K 549 TRP cc_start: 0.7933 (m-10) cc_final: 0.7536 (m-90) REVERT: K 616 ILE cc_start: 0.7272 (tp) cc_final: 0.6894 (tp) REVERT: L 206 GLN cc_start: 0.8097 (mt0) cc_final: 0.7660 (tm-30) REVERT: L 229 MET cc_start: 0.7527 (ptp) cc_final: 0.6031 (ptp) REVERT: L 268 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7893 (tm-30) REVERT: L 315 MET cc_start: 0.8203 (ttt) cc_final: 0.7898 (ttm) REVERT: L 428 ILE cc_start: 0.7693 (mp) cc_final: 0.7490 (mp) REVERT: L 442 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7416 (mtm-85) REVERT: L 598 LEU cc_start: 0.7436 (tt) cc_final: 0.6749 (tt) outliers start: 2 outliers final: 0 residues processed: 317 average time/residue: 0.1652 time to fit residues: 77.4337 Evaluate side-chains 213 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 20.0000 chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 105 optimal weight: 0.0070 chunk 104 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS F 64 ASN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 462 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.100522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.067300 restraints weight = 71337.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.068971 restraints weight = 38951.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069966 restraints weight = 27359.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070507 restraints weight = 22609.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.070737 restraints weight = 20569.992| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20028 Z= 0.227 Angle : 0.691 12.388 28253 Z= 0.378 Chirality : 0.041 0.218 3185 Planarity : 0.005 0.042 2576 Dihedral : 27.793 179.960 4914 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.46 % Rotamer: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % 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 aren not related in a simple way. whole: -0.07 (0.21), residues: 1622 helix: 1.29 (0.17), residues: 934 sheet: -1.89 (0.44), residues: 128 loop : -1.91 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 580 TYR 0.014 0.002 TYR C 51 PHE 0.020 0.002 PHE K 240 TRP 0.010 0.001 TRP K 265 HIS 0.008 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00510 (20028) covalent geometry : angle 0.69113 (28253) hydrogen bonds : bond 0.06273 ( 914) hydrogen bonds : angle 3.86638 ( 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 260 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7770 (pp20) cc_final: 0.7348 (pp20) REVERT: B 74 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8315 (mm-30) REVERT: C 62 GLU cc_start: 0.7727 (tp30) cc_final: 0.7403 (tp30) REVERT: C 65 GLU cc_start: 0.8420 (pt0) cc_final: 0.7607 (pt0) REVERT: D 72 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8326 (tm-30) REVERT: D 84 MET cc_start: 0.8934 (tpp) cc_final: 0.8648 (tpp) REVERT: E 120 MET cc_start: 0.8751 (mpp) cc_final: 0.8494 (mtp) REVERT: K 241 LEU cc_start: 0.6935 (mm) cc_final: 0.6604 (pp) REVERT: K 469 GLU cc_start: 0.7285 (pt0) cc_final: 0.6903 (tp30) REVERT: K 549 TRP cc_start: 0.8185 (m-10) cc_final: 0.7625 (m-90) REVERT: K 559 TYR cc_start: 0.6383 (t80) cc_final: 0.5664 (t80) REVERT: L 206 GLN cc_start: 0.8176 (mt0) cc_final: 0.7754 (tm-30) REVERT: L 229 MET cc_start: 0.7616 (ptp) cc_final: 0.6534 (ptp) REVERT: L 238 ILE cc_start: 0.8147 (mm) cc_final: 0.7914 (mm) REVERT: L 268 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7763 (tm-30) REVERT: L 315 MET cc_start: 0.8401 (ttt) cc_final: 0.8115 (ttm) REVERT: L 448 MET cc_start: 0.8172 (mpp) cc_final: 0.7935 (mpp) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.1549 time to fit residues: 60.9204 Evaluate side-chains 192 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 4.9990 chunk 143 optimal weight: 3.9990 chunk 172 optimal weight: 50.0000 chunk 26 optimal weight: 8.9990 chunk 139 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 184 optimal weight: 0.0970 chunk 120 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN F 64 ASN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.101093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068130 restraints weight = 71167.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069829 restraints weight = 37934.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.070830 restraints weight = 26597.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071402 restraints weight = 21837.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071676 restraints weight = 19782.386| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20028 Z= 0.170 Angle : 0.629 12.210 28253 Z= 0.345 Chirality : 0.038 0.157 3185 Planarity : 0.004 0.040 2576 Dihedral : 27.608 175.134 4914 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 0.07 % Allowed : 1.68 % 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 aren not related in a simple way. whole: 0.16 (0.21), residues: 1622 helix: 1.51 (0.17), residues: 944 sheet: -2.04 (0.43), residues: 134 loop : -1.87 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 89 TYR 0.034 0.002 TYR B 88 PHE 0.016 0.001 PHE K 240 TRP 0.017 0.001 TRP K 265 HIS 0.007 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00375 (20028) covalent geometry : angle 0.62931 (28253) hydrogen bonds : bond 0.05354 ( 914) hydrogen bonds : angle 3.60045 ( 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 268 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8538 (m) cc_final: 0.8189 (p) REVERT: A 53 LYS cc_start: 0.9691 (ttpt) cc_final: 0.9425 (ttpp) REVERT: A 59 GLU cc_start: 0.7937 (pp20) cc_final: 0.7313 (pp20) REVERT: A 64 LYS cc_start: 0.8935 (mptt) cc_final: 0.8660 (mmtp) REVERT: B 88 TYR cc_start: 0.8526 (m-10) cc_final: 0.8089 (m-10) REVERT: C 33 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8116 (ttp80) REVERT: C 62 GLU cc_start: 0.7647 (tp30) cc_final: 0.7252 (tp30) REVERT: C 65 GLU cc_start: 0.8421 (pt0) cc_final: 0.7740 (pt0) REVERT: D 72 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8327 (tm-30) REVERT: E 120 MET cc_start: 0.8749 (mpp) cc_final: 0.8425 (mtp) REVERT: F 64 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8619 (t0) REVERT: F 88 TYR cc_start: 0.8776 (m-10) cc_final: 0.8248 (m-10) REVERT: G 58 TYR cc_start: 0.7720 (t80) cc_final: 0.7472 (t80) REVERT: G 62 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7008 (mt-10) REVERT: K 241 LEU cc_start: 0.7022 (mm) cc_final: 0.6685 (pp) REVERT: K 469 GLU cc_start: 0.7167 (pt0) cc_final: 0.6754 (tp30) REVERT: L 206 GLN cc_start: 0.8164 (mt0) cc_final: 0.7793 (tm-30) REVERT: L 229 MET cc_start: 0.7486 (ptp) cc_final: 0.6617 (ptp) REVERT: L 268 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7750 (tm-30) REVERT: L 315 MET cc_start: 0.8396 (ttt) cc_final: 0.8114 (ttm) REVERT: L 428 ILE cc_start: 0.7648 (mp) cc_final: 0.7431 (mp) REVERT: L 446 ILE cc_start: 0.7549 (mp) cc_final: 0.7021 (tp) REVERT: L 448 MET cc_start: 0.8097 (mpp) cc_final: 0.7679 (mpp) outliers start: 1 outliers final: 0 residues processed: 268 average time/residue: 0.1575 time to fit residues: 63.3273 Evaluate side-chains 191 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 10.0000 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN E 93 GLN F 93 GLN ** K 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 = 0.3810 r_free = 0.3810 target = 0.101816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069339 restraints weight = 70849.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.071019 restraints weight = 39035.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071993 restraints weight = 27477.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072474 restraints weight = 22780.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072811 restraints weight = 20839.198| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20028 Z= 0.146 Angle : 0.609 11.529 28253 Z= 0.335 Chirality : 0.037 0.165 3185 Planarity : 0.004 0.040 2576 Dihedral : 27.430 175.630 4914 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.04 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.22), residues: 1622 helix: 1.78 (0.18), residues: 946 sheet: -1.75 (0.44), residues: 132 loop : -1.72 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 107 TYR 0.012 0.001 TYR L 329 PHE 0.017 0.001 PHE K 240 TRP 0.020 0.001 TRP K 265 HIS 0.006 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00318 (20028) covalent geometry : angle 0.60949 (28253) hydrogen bonds : bond 0.04970 ( 914) hydrogen bonds : angle 3.41565 ( 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 273 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8520 (m) cc_final: 0.8196 (p) REVERT: A 53 LYS cc_start: 0.9694 (ttpt) cc_final: 0.9432 (ttpp) REVERT: A 59 GLU cc_start: 0.7831 (pp20) cc_final: 0.7363 (pp20) REVERT: A 64 LYS cc_start: 0.8889 (mptt) cc_final: 0.8612 (mmtp) REVERT: B 88 TYR cc_start: 0.8741 (m-10) cc_final: 0.8021 (m-10) REVERT: C 62 GLU cc_start: 0.7594 (tp30) cc_final: 0.7097 (tp30) REVERT: C 65 GLU cc_start: 0.8377 (pt0) cc_final: 0.7760 (pt0) REVERT: D 72 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8388 (tm-30) REVERT: D 84 MET cc_start: 0.8773 (tpp) cc_final: 0.8429 (tpp) REVERT: D 93 ASP cc_start: 0.8597 (t70) cc_final: 0.8385 (t0) REVERT: E 120 MET cc_start: 0.8781 (mpp) cc_final: 0.8330 (mtp) REVERT: F 88 TYR cc_start: 0.8679 (m-10) cc_final: 0.8426 (m-10) REVERT: G 62 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7123 (mt-10) REVERT: H 110 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7845 (mmmm) REVERT: K 241 LEU cc_start: 0.6942 (mm) cc_final: 0.6689 (pp) REVERT: K 469 GLU cc_start: 0.7114 (pt0) cc_final: 0.6725 (tp30) REVERT: K 556 MET cc_start: 0.6552 (ptp) cc_final: 0.6276 (ptp) REVERT: K 617 LEU cc_start: 0.7414 (tt) cc_final: 0.6655 (mm) REVERT: L 206 GLN cc_start: 0.8114 (mt0) cc_final: 0.7772 (tm-30) REVERT: L 229 MET cc_start: 0.7547 (ptp) cc_final: 0.6700 (ptp) REVERT: L 238 ILE cc_start: 0.8197 (mm) cc_final: 0.7997 (mm) REVERT: L 268 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7746 (tm-30) REVERT: L 315 MET cc_start: 0.8336 (ttt) cc_final: 0.8080 (ttm) REVERT: L 432 MET cc_start: 0.6610 (mmm) cc_final: 0.6368 (tpp) REVERT: L 446 ILE cc_start: 0.7580 (mp) cc_final: 0.7016 (tp) REVERT: L 448 MET cc_start: 0.8109 (mpp) cc_final: 0.7705 (mpp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1614 time to fit residues: 66.5090 Evaluate side-chains 193 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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: 0.0970 chunk 160 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 136 optimal weight: 40.0000 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 76 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 336 HIS K 629 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.100466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068186 restraints weight = 71494.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069911 restraints weight = 38640.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070892 restraints weight = 26922.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071446 restraints weight = 22197.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.071693 restraints weight = 20135.067| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20028 Z= 0.167 Angle : 0.621 11.960 28253 Z= 0.341 Chirality : 0.038 0.273 3185 Planarity : 0.004 0.044 2576 Dihedral : 27.416 175.239 4914 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.22), residues: 1622 helix: 1.78 (0.17), residues: 944 sheet: -1.65 (0.47), residues: 116 loop : -1.62 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 601 TYR 0.018 0.001 TYR D 65 PHE 0.021 0.001 PHE D 90 TRP 0.029 0.002 TRP K 265 HIS 0.007 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00371 (20028) covalent geometry : angle 0.62058 (28253) hydrogen bonds : bond 0.05311 ( 914) hydrogen bonds : angle 3.49427 ( 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 258 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9705 (ttpt) cc_final: 0.9487 (ttpp) REVERT: A 59 GLU cc_start: 0.7704 (pp20) cc_final: 0.7398 (pp20) REVERT: A 64 LYS cc_start: 0.8862 (mptt) cc_final: 0.8619 (mmtp) REVERT: C 62 GLU cc_start: 0.7477 (tp30) cc_final: 0.6973 (tp30) REVERT: C 65 GLU cc_start: 0.8364 (pt0) cc_final: 0.7654 (pt0) REVERT: C 109 MET cc_start: 0.7917 (ptp) cc_final: 0.7332 (ptp) REVERT: D 72 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8440 (tm-30) REVERT: D 84 MET cc_start: 0.8882 (tpp) cc_final: 0.8625 (tpp) REVERT: E 120 MET cc_start: 0.8736 (mpp) cc_final: 0.8430 (mtp) REVERT: F 88 TYR cc_start: 0.8718 (m-10) cc_final: 0.8468 (m-10) REVERT: K 241 LEU cc_start: 0.6991 (mm) cc_final: 0.6725 (pp) REVERT: K 292 ARG cc_start: 0.7151 (mpp-170) cc_final: 0.6634 (mmm160) REVERT: K 348 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6887 (mt-10) REVERT: K 469 GLU cc_start: 0.7281 (pt0) cc_final: 0.6872 (tp30) REVERT: K 556 MET cc_start: 0.6645 (ptp) cc_final: 0.6388 (ptp) REVERT: L 206 GLN cc_start: 0.8115 (mt0) cc_final: 0.7779 (tm-30) REVERT: L 268 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7746 (tm-30) REVERT: L 315 MET cc_start: 0.8330 (ttt) cc_final: 0.8101 (ttm) REVERT: L 432 MET cc_start: 0.6662 (mmm) cc_final: 0.6413 (tpp) REVERT: L 446 ILE cc_start: 0.7633 (mp) cc_final: 0.7073 (tp) REVERT: L 448 MET cc_start: 0.7998 (mpp) cc_final: 0.7590 (mpp) REVERT: L 632 ASP cc_start: 0.7894 (m-30) cc_final: 0.7166 (t0) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1454 time to fit residues: 58.0530 Evaluate side-chains 188 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 141 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 HIS E 93 GLN F 93 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.097254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066043 restraints weight = 71568.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.067071 restraints weight = 42308.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067361 restraints weight = 29145.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067815 restraints weight = 24622.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067729 restraints weight = 23152.897| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.7854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20028 Z= 0.264 Angle : 0.724 13.098 28253 Z= 0.393 Chirality : 0.042 0.210 3185 Planarity : 0.005 0.047 2576 Dihedral : 27.707 172.750 4914 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.54 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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 aren not related in a simple way. whole: 0.02 (0.21), residues: 1622 helix: 1.29 (0.17), residues: 946 sheet: -1.99 (0.44), residues: 118 loop : -1.77 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 117 TYR 0.031 0.002 TYR D 65 PHE 0.016 0.002 PHE D 90 TRP 0.050 0.003 TRP K 265 HIS 0.010 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00601 (20028) covalent geometry : angle 0.72372 (28253) hydrogen bonds : bond 0.06614 ( 914) hydrogen bonds : angle 3.98544 ( 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 240 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9681 (ttpt) cc_final: 0.9461 (ttpp) REVERT: A 59 GLU cc_start: 0.7698 (pp20) cc_final: 0.7360 (pp20) REVERT: B 84 MET cc_start: 0.8298 (tpt) cc_final: 0.7987 (tmm) REVERT: C 62 GLU cc_start: 0.7533 (tp30) cc_final: 0.7144 (tp30) REVERT: C 65 GLU cc_start: 0.8354 (pt0) cc_final: 0.7698 (pt0) REVERT: D 87 MET cc_start: 0.9149 (mmm) cc_final: 0.8911 (tpp) REVERT: E 120 MET cc_start: 0.8716 (mpp) cc_final: 0.8490 (mtp) REVERT: G 58 TYR cc_start: 0.7688 (t80) cc_final: 0.7204 (t80) REVERT: G 62 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6915 (mt-10) REVERT: K 241 LEU cc_start: 0.7119 (mm) cc_final: 0.6781 (pp) REVERT: K 292 ARG cc_start: 0.7020 (mpp-170) cc_final: 0.6479 (mmm160) REVERT: K 469 GLU cc_start: 0.7580 (pt0) cc_final: 0.6934 (tp30) REVERT: K 556 MET cc_start: 0.6539 (ptp) cc_final: 0.6241 (ptp) REVERT: L 206 GLN cc_start: 0.8282 (mt0) cc_final: 0.7869 (tm-30) REVERT: L 268 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7751 (tm-30) REVERT: L 295 HIS cc_start: 0.4495 (t70) cc_final: 0.3610 (t70) REVERT: L 446 ILE cc_start: 0.8070 (mp) cc_final: 0.7806 (pt) REVERT: L 448 MET cc_start: 0.7739 (mpp) cc_final: 0.7432 (mpp) REVERT: L 614 THR cc_start: 0.8557 (p) cc_final: 0.8142 (t) REVERT: L 632 ASP cc_start: 0.7905 (m-30) cc_final: 0.7157 (t0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1545 time to fit residues: 56.2017 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 : 0.635 ------------------------------------------------------------------------------- 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: 10.0000 chunk 174 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 74 HIS ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.097970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066948 restraints weight = 71407.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068029 restraints weight = 41612.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068397 restraints weight = 28620.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068754 restraints weight = 23852.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068753 restraints weight = 22600.880| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.8027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20028 Z= 0.201 Angle : 0.669 12.646 28253 Z= 0.365 Chirality : 0.040 0.198 3185 Planarity : 0.004 0.048 2576 Dihedral : 27.669 174.175 4914 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.67 % Favored : 94.27 % Rotamer: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.65 % 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 aren not related in a simple way. whole: 0.18 (0.21), residues: 1622 helix: 1.45 (0.17), residues: 946 sheet: -2.04 (0.44), residues: 118 loop : -1.75 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 83 TYR 0.024 0.002 TYR D 65 PHE 0.017 0.001 PHE D 90 TRP 0.043 0.002 TRP K 265 HIS 0.008 0.001 HIS K 295 Details of bonding type rmsd covalent geometry : bond 0.00454 (20028) covalent geometry : angle 0.66921 (28253) hydrogen bonds : bond 0.05835 ( 914) hydrogen bonds : angle 3.74166 ( 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 247 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9680 (ttpt) cc_final: 0.9437 (ttpp) REVERT: A 59 GLU cc_start: 0.7715 (pp20) cc_final: 0.7371 (pp20) REVERT: B 84 MET cc_start: 0.8283 (tpt) cc_final: 0.8075 (mmm) REVERT: C 65 GLU cc_start: 0.8397 (pt0) cc_final: 0.7823 (pt0) REVERT: D 72 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8499 (tm-30) REVERT: D 84 MET cc_start: 0.8975 (tpp) cc_final: 0.8640 (tpp) REVERT: E 120 MET cc_start: 0.8757 (mpp) cc_final: 0.8488 (mtp) REVERT: G 58 TYR cc_start: 0.7715 (t80) cc_final: 0.7427 (t80) REVERT: G 62 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7042 (mt-10) REVERT: K 241 LEU cc_start: 0.7090 (mm) cc_final: 0.6779 (pp) REVERT: K 292 ARG cc_start: 0.7026 (mpp-170) cc_final: 0.6519 (mmm160) REVERT: K 348 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7213 (mm-30) REVERT: K 469 GLU cc_start: 0.7588 (pt0) cc_final: 0.6995 (tp30) REVERT: K 556 MET cc_start: 0.6588 (ptp) cc_final: 0.6309 (ptp) REVERT: L 206 GLN cc_start: 0.8276 (mt0) cc_final: 0.7847 (tm-30) REVERT: L 268 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7825 (tm-30) REVERT: L 295 HIS cc_start: 0.4444 (t70) cc_final: 0.3935 (t70) REVERT: L 432 MET cc_start: 0.6624 (mmm) cc_final: 0.6417 (tpp) REVERT: L 446 ILE cc_start: 0.8106 (mp) cc_final: 0.7827 (pt) REVERT: L 448 MET cc_start: 0.7818 (mpp) cc_final: 0.7541 (mpp) REVERT: L 614 THR cc_start: 0.8463 (p) cc_final: 0.8010 (t) REVERT: L 632 ASP cc_start: 0.7843 (m-30) cc_final: 0.7093 (t0) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.1552 time to fit residues: 57.9478 Evaluate side-chains 187 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 5.9990 chunk 171 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 chunk 19 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN G 85 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 ASN L 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.099930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.067224 restraints weight = 72296.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068964 restraints weight = 38367.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069990 restraints weight = 26492.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070569 restraints weight = 21758.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070843 restraints weight = 19650.283| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.8162 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= 0.144 Angle : 0.626 12.001 28253 Z= 0.340 Chirality : 0.037 0.182 3185 Planarity : 0.004 0.047 2576 Dihedral : 27.480 175.539 4914 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.49 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 aren not related in a simple way. whole: 0.65 (0.22), residues: 1622 helix: 1.84 (0.17), residues: 932 sheet: -1.47 (0.49), residues: 96 loop : -1.58 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 83 TYR 0.017 0.001 TYR D 65 PHE 0.017 0.001 PHE D 90 TRP 0.033 0.002 TRP K 265 HIS 0.006 0.001 HIS K 499 Details of bonding type rmsd covalent geometry : bond 0.00313 (20028) covalent geometry : angle 0.62588 (28253) hydrogen bonds : bond 0.05120 ( 914) hydrogen bonds : angle 3.48711 ( 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 257 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9667 (ttpt) cc_final: 0.9412 (ttpp) REVERT: A 59 GLU cc_start: 0.7655 (pp20) cc_final: 0.7325 (pp20) REVERT: C 62 GLU cc_start: 0.7536 (tp30) cc_final: 0.7301 (tp30) REVERT: D 72 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8531 (tm-30) REVERT: D 84 MET cc_start: 0.8727 (tpp) cc_final: 0.8388 (tpp) REVERT: E 56 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8806 (tptt) REVERT: G 42 GLU cc_start: 0.8275 (pp20) cc_final: 0.7898 (pp20) REVERT: K 241 LEU cc_start: 0.7106 (mm) cc_final: 0.6832 (pp) REVERT: K 292 ARG cc_start: 0.7032 (mpp-170) cc_final: 0.6512 (mmm160) REVERT: K 348 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7202 (mm-30) REVERT: K 373 TRP cc_start: 0.6728 (t60) cc_final: 0.6494 (t60) REVERT: K 469 GLU cc_start: 0.7650 (pt0) cc_final: 0.7019 (tp30) REVERT: K 556 MET cc_start: 0.6526 (ptp) cc_final: 0.6264 (ptp) REVERT: K 601 ARG cc_start: 0.7392 (ptt180) cc_final: 0.7068 (ptt90) REVERT: L 206 GLN cc_start: 0.8139 (mt0) cc_final: 0.7846 (tm-30) REVERT: L 268 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7843 (tm-30) REVERT: L 315 MET cc_start: 0.8311 (ttm) cc_final: 0.7776 (mtm) REVERT: L 446 ILE cc_start: 0.8129 (mp) cc_final: 0.7885 (pt) REVERT: L 448 MET cc_start: 0.7977 (mpp) cc_final: 0.7709 (mpp) REVERT: L 614 THR cc_start: 0.8469 (p) cc_final: 0.7989 (t) REVERT: L 632 ASP cc_start: 0.7850 (m-30) cc_final: 0.7146 (t0) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1602 time to fit residues: 61.5760 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 : 0.623 ------------------------------------------------------------------------------- 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: 7.9990 chunk 68 optimal weight: 0.4980 chunk 122 optimal weight: 0.0000 chunk 85 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 170 optimal weight: 0.1980 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 121 optimal weight: 0.4980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 415 GLN K 629 GLN L 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.101607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069920 restraints weight = 71868.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071676 restraints weight = 38198.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.072700 restraints weight = 26213.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073287 restraints weight = 21440.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.073558 restraints weight = 19310.755| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.8362 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= 0.136 Angle : 0.607 11.265 28253 Z= 0.330 Chirality : 0.037 0.197 3185 Planarity : 0.004 0.047 2576 Dihedral : 27.229 176.220 4914 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % 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 aren not related in a simple way. whole: 0.96 (0.22), residues: 1622 helix: 2.06 (0.18), residues: 930 sheet: -1.02 (0.52), residues: 94 loop : -1.45 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 107 TYR 0.015 0.001 TYR B 88 PHE 0.016 0.001 PHE D 90 TRP 0.026 0.002 TRP K 373 HIS 0.012 0.001 HIS K 295 Details of bonding type rmsd covalent geometry : bond 0.00292 (20028) covalent geometry : angle 0.60652 (28253) hydrogen bonds : bond 0.04621 ( 914) hydrogen bonds : angle 3.31925 ( 2423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3898.32 seconds wall clock time: 68 minutes 1.51 seconds (4081.51 seconds total)