Starting phenix.real_space_refine on Mon Jun 16 12:00:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wha_37537/06_2025/8wha_37537_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wha_37537/06_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_37537/06_2025/8wha_37537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wha_37537/06_2025/8wha_37537.map" model { file = "/net/cci-nas-00/data/ceres_data/8wha_37537/06_2025/8wha_37537_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wha_37537/06_2025/8wha_37537_neut.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.45, per 1000 atoms: 0.55 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: 4.36 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 7.29 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: 7.68 Time building geometry restraints manager: 5.25 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: 1.060 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: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.360 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (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 TRP 0.038 0.002 TRP K 217 HIS 0.014 0.002 HIS K 541 PHE 0.048 0.003 PHE C 26 TYR 0.041 0.003 TYR L 329 ARG 0.008 0.001 ARG G 89 Details of bonding type rmsd hydrogen bonds : bond 0.22885 ( 914) hydrogen bonds : angle 9.11710 ( 2423) covalent geometry : bond 0.01006 (20028) covalent geometry : angle 1.29474 (28253) *********************** 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 : 1.595 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: 0.4167 time to fit residues: 316.5774 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 : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 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 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 548 GLN 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 = 0.3816 r_free = 0.3816 target = 0.103193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.071409 restraints weight = 70945.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072866 restraints weight = 43396.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.073284 restraints weight = 25924.438| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 20028 Z= 0.303 Angle : 0.832 10.859 28253 Z= 0.449 Chirality : 0.047 0.301 3185 Planarity : 0.006 0.057 2576 Dihedral : 28.412 179.940 4914 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.35 % Favored : 93.53 % Rotamer: Outliers : 0.14 % Allowed : 5.54 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1622 helix: 0.23 (0.17), residues: 923 sheet: -2.36 (0.42), residues: 132 loop : -2.38 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP K 622 HIS 0.009 0.002 HIS K 635 PHE 0.025 0.003 PHE K 240 TYR 0.030 0.002 TYR D 108 ARG 0.025 0.001 ARG F 19 Details of bonding type rmsd hydrogen bonds : bond 0.07384 ( 914) hydrogen bonds : angle 4.35466 ( 2423) covalent geometry : bond 0.00689 (20028) covalent geometry : angle 0.83211 (28253) *********************** 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 325 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.5610 (mpt180) cc_final: 0.5311 (mpt180) REVERT: A 59 GLU cc_start: 0.8117 (pp20) cc_final: 0.7449 (pp20) REVERT: A 68 GLN cc_start: 0.8732 (tt0) cc_final: 0.8434 (mt0) REVERT: A 77 ASP cc_start: 0.8605 (p0) cc_final: 0.8333 (p0) REVERT: C 25 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8388 (mm-40) REVERT: D 81 SER cc_start: 0.9055 (t) cc_final: 0.8755 (m) REVERT: E 120 MET cc_start: 0.8564 (mpp) cc_final: 0.8343 (mtp) REVERT: H 76 ASP cc_start: 0.8336 (p0) cc_final: 0.8096 (p0) REVERT: K 229 MET cc_start: 0.4205 (ptt) cc_final: 0.3685 (ptt) REVERT: K 241 LEU cc_start: 0.6454 (mm) cc_final: 0.6129 (pp) REVERT: K 312 GLU cc_start: 0.8593 (mp0) cc_final: 0.8232 (mp0) REVERT: K 329 TYR cc_start: 0.6118 (m-80) cc_final: 0.5494 (m-80) REVERT: K 348 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7004 (mm-30) REVERT: K 469 GLU cc_start: 0.7190 (pt0) cc_final: 0.6827 (tp30) REVERT: K 487 ASN cc_start: 0.7902 (t0) cc_final: 0.7480 (p0) REVERT: K 506 GLN cc_start: 0.7807 (pt0) cc_final: 0.7586 (pp30) REVERT: K 549 TRP cc_start: 0.7771 (m-10) cc_final: 0.7442 (m-90) REVERT: K 559 TYR cc_start: 0.4659 (t80) cc_final: 0.4372 (t80) REVERT: K 617 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7172 (tp) REVERT: L 315 MET cc_start: 0.8427 (ttt) cc_final: 0.8189 (ttm) REVERT: L 442 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7303 (mtm-85) REVERT: L 580 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8598 (tmt-80) REVERT: L 660 LYS cc_start: 0.8441 (tttt) cc_final: 0.8211 (mttt) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 0.3376 time to fit residues: 159.7067 Evaluate side-chains 207 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN F 18 HIS ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 496 ASN ** L 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 625 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.099082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.066078 restraints weight = 71005.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067749 restraints weight = 38978.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068693 restraints weight = 27462.117| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 20028 Z= 0.297 Angle : 0.782 13.141 28253 Z= 0.424 Chirality : 0.044 0.177 3185 Planarity : 0.006 0.047 2576 Dihedral : 28.150 178.547 4914 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1622 helix: 0.59 (0.17), residues: 944 sheet: -2.41 (0.40), residues: 134 loop : -2.23 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 265 HIS 0.017 0.002 HIS K 635 PHE 0.026 0.002 PHE K 240 TYR 0.043 0.003 TYR D 108 ARG 0.009 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.07135 ( 914) hydrogen bonds : angle 4.23402 ( 2423) covalent geometry : bond 0.00677 (20028) covalent geometry : angle 0.78186 (28253) *********************** 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 268 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8187 (pp20) cc_final: 0.7529 (pp20) REVERT: A 68 GLN cc_start: 0.8741 (tt0) cc_final: 0.8416 (mt0) REVERT: C 65 GLU cc_start: 0.8472 (pt0) cc_final: 0.7833 (pt0) REVERT: C 91 ASP cc_start: 0.8510 (t0) cc_final: 0.8302 (t0) REVERT: D 72 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8390 (tm-30) REVERT: D 84 MET cc_start: 0.9006 (tpp) cc_final: 0.8608 (tpp) REVERT: E 120 MET cc_start: 0.8728 (mpp) cc_final: 0.8338 (mtp) REVERT: G 42 GLU cc_start: 0.8113 (pp20) cc_final: 0.7748 (pp20) REVERT: G 58 TYR cc_start: 0.7833 (t80) cc_final: 0.7099 (t80) REVERT: G 62 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7176 (mt-10) REVERT: K 241 LEU cc_start: 0.6973 (mm) cc_final: 0.6620 (pp) REVERT: K 469 GLU cc_start: 0.7603 (pt0) cc_final: 0.7079 (tp30) REVERT: K 487 ASN cc_start: 0.7599 (t0) cc_final: 0.7282 (m110) REVERT: K 491 ILE cc_start: 0.8352 (mm) cc_final: 0.8092 (tp) REVERT: K 549 TRP cc_start: 0.8077 (m-10) cc_final: 0.7542 (m-90) REVERT: K 616 ILE cc_start: 0.7355 (tp) cc_final: 0.7004 (tp) REVERT: L 206 GLN cc_start: 0.8233 (mt0) cc_final: 0.7771 (tm-30) REVERT: L 229 MET cc_start: 0.7583 (ptp) cc_final: 0.6015 (ptp) REVERT: L 315 MET cc_start: 0.8466 (ttt) cc_final: 0.8209 (ttm) REVERT: L 660 LYS cc_start: 0.8337 (tttt) cc_final: 0.8119 (mttt) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3232 time to fit residues: 128.9193 Evaluate side-chains 178 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 172 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.096998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.065734 restraints weight = 71966.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.066922 restraints weight = 45217.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067503 restraints weight = 28127.651| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.7081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 20028 Z= 0.307 Angle : 0.774 13.406 28253 Z= 0.419 Chirality : 0.044 0.215 3185 Planarity : 0.005 0.046 2576 Dihedral : 28.021 177.831 4914 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1622 helix: 0.79 (0.17), residues: 937 sheet: -2.56 (0.41), residues: 114 loop : -2.08 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 265 HIS 0.013 0.002 HIS K 295 PHE 0.018 0.002 PHE K 240 TYR 0.014 0.002 TYR C 58 ARG 0.022 0.001 ARG G 89 Details of bonding type rmsd hydrogen bonds : bond 0.07013 ( 914) hydrogen bonds : angle 4.22596 ( 2423) covalent geometry : bond 0.00700 (20028) covalent geometry : angle 0.77430 (28253) *********************** 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 237 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9667 (ttpt) cc_final: 0.9429 (ttpp) REVERT: A 59 GLU cc_start: 0.7855 (pp20) cc_final: 0.7371 (pp20) REVERT: A 68 GLN cc_start: 0.8672 (tt0) cc_final: 0.8377 (mt0) REVERT: C 62 GLU cc_start: 0.7620 (tp30) cc_final: 0.7134 (tp30) REVERT: C 65 GLU cc_start: 0.8220 (pt0) cc_final: 0.7485 (pt0) REVERT: D 72 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8488 (tm-30) REVERT: D 84 MET cc_start: 0.8918 (tpp) cc_final: 0.8570 (tpp) REVERT: E 120 MET cc_start: 0.8773 (mpp) cc_final: 0.8493 (mtp) REVERT: F 88 TYR cc_start: 0.8707 (m-10) cc_final: 0.8465 (m-10) REVERT: G 58 TYR cc_start: 0.7996 (t80) cc_final: 0.7561 (t80) REVERT: K 241 LEU cc_start: 0.6911 (mm) cc_final: 0.6527 (pp) REVERT: K 259 LEU cc_start: 0.8087 (mp) cc_final: 0.7877 (mp) REVERT: K 312 GLU cc_start: 0.8851 (mp0) cc_final: 0.8167 (mp0) REVERT: K 469 GLU cc_start: 0.7477 (pt0) cc_final: 0.6862 (tp30) REVERT: K 487 ASN cc_start: 0.7579 (t0) cc_final: 0.7050 (p0) REVERT: K 556 MET cc_start: 0.6652 (ptp) cc_final: 0.6335 (ptp) REVERT: L 206 GLN cc_start: 0.8293 (mt0) cc_final: 0.7866 (tm-30) REVERT: L 229 MET cc_start: 0.7524 (ptp) cc_final: 0.6764 (ptp) REVERT: L 428 ILE cc_start: 0.7533 (mp) cc_final: 0.7325 (mp) REVERT: L 446 ILE cc_start: 0.7770 (mp) cc_final: 0.7298 (tp) REVERT: L 598 LEU cc_start: 0.7841 (tt) cc_final: 0.7510 (tt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3140 time to fit residues: 111.8635 Evaluate side-chains 172 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 236 GLN L 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.099594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067131 restraints weight = 71556.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068833 restraints weight = 38383.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069850 restraints weight = 26692.226| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.7250 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= 0.153 Angle : 0.634 13.015 28253 Z= 0.348 Chirality : 0.039 0.161 3185 Planarity : 0.004 0.041 2576 Dihedral : 27.769 176.179 4914 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1622 helix: 1.47 (0.17), residues: 923 sheet: -2.29 (0.42), residues: 112 loop : -1.84 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 265 HIS 0.012 0.001 HIS K 295 PHE 0.013 0.001 PHE K 240 TYR 0.026 0.002 TYR H 108 ARG 0.007 0.000 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 914) hydrogen bonds : angle 3.60691 ( 2423) covalent geometry : bond 0.00333 (20028) covalent geometry : angle 0.63436 (28253) *********************** 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 271 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.978 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: 0.9657 (ttpt) cc_final: 0.9417 (ttpp) REVERT: A 59 GLU cc_start: 0.7814 (pp20) cc_final: 0.7287 (pp20) REVERT: A 64 LYS cc_start: 0.8971 (mptt) cc_final: 0.8519 (mmtp) REVERT: C 62 GLU cc_start: 0.7607 (tp30) cc_final: 0.7281 (tp30) REVERT: C 65 GLU cc_start: 0.8370 (pt0) cc_final: 0.7843 (pt0) REVERT: D 72 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8457 (tm-30) REVERT: E 120 MET cc_start: 0.8772 (mpp) cc_final: 0.8337 (mtp) REVERT: G 42 GLU cc_start: 0.8304 (pp20) cc_final: 0.7972 (pp20) REVERT: G 58 TYR cc_start: 0.7775 (t80) cc_final: 0.7470 (t80) REVERT: G 62 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7437 (mt-10) REVERT: K 241 LEU cc_start: 0.7062 (mm) cc_final: 0.6715 (pp) REVERT: K 292 ARG cc_start: 0.7111 (mpp-170) cc_final: 0.6647 (mmm160) REVERT: K 312 GLU cc_start: 0.8893 (mp0) cc_final: 0.8670 (mt-10) REVERT: K 469 GLU cc_start: 0.7583 (pt0) cc_final: 0.7001 (tp30) REVERT: L 206 GLN cc_start: 0.8139 (mt0) cc_final: 0.7816 (tm-30) REVERT: L 268 GLU cc_start: 0.7865 (tp30) cc_final: 0.7557 (tm-30) REVERT: L 428 ILE cc_start: 0.7550 (mp) cc_final: 0.7337 (mp) REVERT: L 446 ILE cc_start: 0.7858 (mp) cc_final: 0.7312 (tp) REVERT: L 598 LEU cc_start: 0.7749 (tt) cc_final: 0.7466 (tt) REVERT: L 660 LYS cc_start: 0.8285 (tttt) cc_final: 0.8050 (mttt) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3276 time to fit residues: 133.7736 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 : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 135 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 635 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.099185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.066754 restraints weight = 71375.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068460 restraints weight = 38092.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069456 restraints weight = 26538.335| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.7558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20028 Z= 0.171 Angle : 0.634 12.591 28253 Z= 0.347 Chirality : 0.038 0.160 3185 Planarity : 0.004 0.048 2576 Dihedral : 27.622 174.945 4914 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1622 helix: 1.67 (0.17), residues: 927 sheet: -2.22 (0.43), residues: 112 loop : -1.72 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 373 HIS 0.010 0.001 HIS K 295 PHE 0.012 0.001 PHE K 240 TYR 0.030 0.002 TYR B 88 ARG 0.006 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.05418 ( 914) hydrogen bonds : angle 3.59981 ( 2423) covalent geometry : bond 0.00377 (20028) covalent geometry : angle 0.63422 (28253) *********************** 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 245 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9674 (ttpt) cc_final: 0.9434 (ttpp) REVERT: C 62 GLU cc_start: 0.7528 (tp30) cc_final: 0.6908 (tp30) REVERT: C 65 GLU cc_start: 0.8333 (pt0) cc_final: 0.7714 (pt0) REVERT: C 109 MET cc_start: 0.7845 (ptp) cc_final: 0.7644 (ptp) REVERT: D 84 MET cc_start: 0.8760 (tpp) cc_final: 0.8501 (tpp) REVERT: E 120 MET cc_start: 0.8712 (mpp) cc_final: 0.8368 (mtp) REVERT: G 42 GLU cc_start: 0.8297 (pp20) cc_final: 0.7941 (pp20) REVERT: G 58 TYR cc_start: 0.7943 (t80) cc_final: 0.7538 (t80) REVERT: G 62 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7538 (mt-10) REVERT: K 241 LEU cc_start: 0.7081 (mm) cc_final: 0.6700 (pp) REVERT: K 265 TRP cc_start: 0.7927 (t60) cc_final: 0.7667 (t60) REVERT: K 469 GLU cc_start: 0.7637 (pt0) cc_final: 0.7032 (tp30) REVERT: K 487 ASN cc_start: 0.7704 (t0) cc_final: 0.7235 (m-40) REVERT: K 506 GLN cc_start: 0.7813 (pt0) cc_final: 0.7441 (pp30) REVERT: K 556 MET cc_start: 0.6520 (ptp) cc_final: 0.6235 (ptp) REVERT: L 206 GLN cc_start: 0.8158 (mt0) cc_final: 0.7815 (tm-30) REVERT: L 238 ILE cc_start: 0.7898 (mt) cc_final: 0.7575 (mt) REVERT: L 268 GLU cc_start: 0.7997 (tp30) cc_final: 0.7637 (tm-30) REVERT: L 315 MET cc_start: 0.8432 (ttm) cc_final: 0.7747 (mtm) REVERT: L 432 MET cc_start: 0.6656 (mmm) cc_final: 0.6402 (tpp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3096 time to fit residues: 113.8916 Evaluate side-chains 177 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 179 optimal weight: 30.0000 chunk 166 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 HIS ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.098125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066144 restraints weight = 70606.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.067717 restraints weight = 39306.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068650 restraints weight = 27972.267| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.004 0.046 20028 Z= 0.189 Angle : 0.651 12.445 28253 Z= 0.355 Chirality : 0.039 0.268 3185 Planarity : 0.004 0.056 2576 Dihedral : 27.616 173.315 4914 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.10 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1622 helix: 1.57 (0.17), residues: 940 sheet: -1.46 (0.52), residues: 88 loop : -1.82 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 373 HIS 0.011 0.001 HIS K 295 PHE 0.012 0.001 PHE K 240 TYR 0.018 0.002 TYR D 65 ARG 0.008 0.001 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.05641 ( 914) hydrogen bonds : angle 3.64561 ( 2423) covalent geometry : bond 0.00422 (20028) covalent geometry : angle 0.65142 (28253) *********************** 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 235 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6518 (mpt180) cc_final: 0.6297 (mmt180) REVERT: A 53 LYS cc_start: 0.9678 (ttpt) cc_final: 0.9447 (ttpp) REVERT: C 62 GLU cc_start: 0.7495 (tp30) cc_final: 0.7038 (tp30) REVERT: C 65 GLU cc_start: 0.8370 (pt0) cc_final: 0.7868 (pt0) REVERT: E 120 MET cc_start: 0.8724 (mpp) cc_final: 0.8317 (mtp) REVERT: G 42 GLU cc_start: 0.8309 (pp20) cc_final: 0.8043 (pp20) REVERT: K 241 LEU cc_start: 0.7238 (mm) cc_final: 0.6854 (pp) REVERT: K 265 TRP cc_start: 0.7891 (t60) cc_final: 0.7607 (t60) REVERT: K 469 GLU cc_start: 0.7701 (pt0) cc_final: 0.7103 (tp30) REVERT: K 506 GLN cc_start: 0.7788 (pt0) cc_final: 0.7373 (pp30) REVERT: K 556 MET cc_start: 0.6607 (ptp) cc_final: 0.6291 (ptp) REVERT: L 206 GLN cc_start: 0.8171 (mt0) cc_final: 0.7834 (tm-30) REVERT: L 238 ILE cc_start: 0.8028 (mt) cc_final: 0.7627 (mt) REVERT: L 268 GLU cc_start: 0.7906 (tp30) cc_final: 0.7535 (tm-30) REVERT: L 295 HIS cc_start: 0.3819 (t70) cc_final: 0.3525 (t70) REVERT: L 432 MET cc_start: 0.6687 (mmm) cc_final: 0.6415 (tpp) REVERT: L 614 THR cc_start: 0.8554 (p) cc_final: 0.8080 (t) REVERT: L 632 ASP cc_start: 0.8039 (m-30) cc_final: 0.6956 (t0) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3041 time to fit residues: 109.9838 Evaluate side-chains 176 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 0 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.097788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064943 restraints weight = 71927.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.066557 restraints weight = 39323.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.067531 restraints weight = 27723.372| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.8183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20028 Z= 0.205 Angle : 0.668 12.786 28253 Z= 0.362 Chirality : 0.040 0.219 3185 Planarity : 0.004 0.045 2576 Dihedral : 27.679 173.066 4914 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1622 helix: 1.53 (0.17), residues: 938 sheet: -1.46 (0.52), residues: 92 loop : -1.83 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 373 HIS 0.009 0.001 HIS K 295 PHE 0.012 0.001 PHE K 240 TYR 0.023 0.002 TYR K 281 ARG 0.016 0.001 ARG L 337 Details of bonding type rmsd hydrogen bonds : bond 0.05810 ( 914) hydrogen bonds : angle 3.72339 ( 2423) covalent geometry : bond 0.00463 (20028) covalent geometry : angle 0.66816 (28253) *********************** 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 233 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9668 (ttpt) cc_final: 0.9428 (ttpp) REVERT: B 84 MET cc_start: 0.8101 (mmm) cc_final: 0.7805 (mmm) REVERT: C 62 GLU cc_start: 0.7508 (tp30) cc_final: 0.7025 (tp30) REVERT: C 65 GLU cc_start: 0.8365 (pt0) cc_final: 0.7838 (pt0) REVERT: C 109 MET cc_start: 0.7922 (ptp) cc_final: 0.7680 (ptp) REVERT: D 84 MET cc_start: 0.9231 (mmp) cc_final: 0.9021 (tpp) REVERT: E 120 MET cc_start: 0.8775 (mpp) cc_final: 0.8497 (mtp) REVERT: K 241 LEU cc_start: 0.7171 (mm) cc_final: 0.6819 (pp) REVERT: K 373 TRP cc_start: 0.6742 (t60) cc_final: 0.6537 (t60) REVERT: K 469 GLU cc_start: 0.7695 (pt0) cc_final: 0.7008 (tp30) REVERT: K 506 GLN cc_start: 0.7728 (pt0) cc_final: 0.7321 (pp30) REVERT: K 549 TRP cc_start: 0.8254 (m-90) cc_final: 0.7710 (m-90) REVERT: L 206 GLN cc_start: 0.8215 (mt0) cc_final: 0.7850 (tm-30) REVERT: L 295 HIS cc_start: 0.4435 (t70) cc_final: 0.4112 (t70) REVERT: L 432 MET cc_start: 0.6708 (mmm) cc_final: 0.6448 (tpp) REVERT: L 614 THR cc_start: 0.8672 (p) cc_final: 0.8207 (t) REVERT: L 632 ASP cc_start: 0.8074 (m-30) cc_final: 0.6997 (t0) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3052 time to fit residues: 108.6292 Evaluate side-chains 179 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 236 GLN ** K 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.096780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.064529 restraints weight = 71376.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.066117 restraints weight = 39205.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067047 restraints weight = 27729.963| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.8463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20028 Z= 0.233 Angle : 0.699 13.994 28253 Z= 0.377 Chirality : 0.041 0.205 3185 Planarity : 0.005 0.047 2576 Dihedral : 27.736 172.941 4914 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1622 helix: 1.40 (0.17), residues: 937 sheet: -1.44 (0.53), residues: 92 loop : -1.87 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 265 HIS 0.010 0.001 HIS K 499 PHE 0.021 0.002 PHE K 459 TYR 0.024 0.002 TYR D 65 ARG 0.006 0.001 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.06077 ( 914) hydrogen bonds : angle 3.87530 ( 2423) covalent geometry : bond 0.00529 (20028) covalent geometry : angle 0.69930 (28253) *********************** 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 217 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9673 (ttpt) cc_final: 0.9435 (ttpp) REVERT: C 62 GLU cc_start: 0.7516 (tp30) cc_final: 0.7136 (tp30) REVERT: C 65 GLU cc_start: 0.8366 (pt0) cc_final: 0.7813 (pt0) REVERT: E 120 MET cc_start: 0.8749 (mpp) cc_final: 0.8450 (mpp) REVERT: G 42 GLU cc_start: 0.8174 (pp20) cc_final: 0.7918 (pp20) REVERT: K 241 LEU cc_start: 0.7396 (mm) cc_final: 0.7013 (pp) REVERT: K 469 GLU cc_start: 0.7716 (pt0) cc_final: 0.7104 (tp30) REVERT: K 506 GLN cc_start: 0.7756 (pt0) cc_final: 0.7380 (pp30) REVERT: K 549 TRP cc_start: 0.8266 (m-90) cc_final: 0.7793 (m-90) REVERT: L 206 GLN cc_start: 0.8189 (mt0) cc_final: 0.7867 (tm-30) REVERT: L 295 HIS cc_start: 0.4469 (t70) cc_final: 0.4071 (t70) REVERT: L 432 MET cc_start: 0.6715 (mmm) cc_final: 0.6464 (tpp) REVERT: L 614 THR cc_start: 0.8722 (p) cc_final: 0.8365 (t) REVERT: L 632 ASP cc_start: 0.8014 (m-30) cc_final: 0.6930 (t70) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3621 time to fit residues: 124.4743 Evaluate side-chains 167 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 33 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN K 282 HIS K 295 HIS K 324 HIS ** K 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.098152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066026 restraints weight = 71308.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067640 restraints weight = 38593.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068617 restraints weight = 27147.661| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.8551 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= 0.166 Angle : 0.648 12.840 28253 Z= 0.352 Chirality : 0.039 0.176 3185 Planarity : 0.004 0.047 2576 Dihedral : 27.587 174.006 4914 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1622 helix: 1.60 (0.17), residues: 938 sheet: -1.58 (0.51), residues: 102 loop : -1.82 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 373 HIS 0.010 0.001 HIS K 282 PHE 0.018 0.001 PHE K 240 TYR 0.027 0.002 TYR H 108 ARG 0.009 0.001 ARG L 657 Details of bonding type rmsd hydrogen bonds : bond 0.05378 ( 914) hydrogen bonds : angle 3.61919 ( 2423) covalent geometry : bond 0.00369 (20028) covalent geometry : angle 0.64796 (28253) ********************** 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 221 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.9655 (ttpt) cc_final: 0.9431 (ttpp) REVERT: A 64 LYS cc_start: 0.8865 (mptt) cc_final: 0.8654 (mmtp) REVERT: C 62 GLU cc_start: 0.7459 (tp30) cc_final: 0.7065 (tp30) REVERT: E 120 MET cc_start: 0.8768 (mpp) cc_final: 0.8450 (mpp) REVERT: G 92 GLU cc_start: 0.7826 (pm20) cc_final: 0.7466 (tp30) REVERT: K 241 LEU cc_start: 0.7249 (mm) cc_final: 0.6952 (pp) REVERT: K 373 TRP cc_start: 0.6759 (t60) cc_final: 0.6550 (t60) REVERT: K 469 GLU cc_start: 0.7827 (pt0) cc_final: 0.7282 (tp30) REVERT: K 506 GLN cc_start: 0.7679 (pt0) cc_final: 0.7355 (pp30) REVERT: K 526 PHE cc_start: 0.8277 (t80) cc_final: 0.7814 (t80) REVERT: L 614 THR cc_start: 0.8711 (p) cc_final: 0.8347 (t) REVERT: L 632 ASP cc_start: 0.8001 (m-30) cc_final: 0.6999 (t70) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3755 time to fit residues: 129.1914 Evaluate side-chains 171 residues out of total 1427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 141 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 chunk 45 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 366 GLN K 623 ASN ** K 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.099736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067388 restraints weight = 72110.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069070 restraints weight = 38851.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070070 restraints weight = 27031.468| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.8668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20028 Z= 0.141 Angle : 0.621 12.289 28253 Z= 0.336 Chirality : 0.037 0.178 3185 Planarity : 0.004 0.047 2576 Dihedral : 27.424 174.524 4914 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1622 helix: 1.88 (0.18), residues: 925 sheet: -1.55 (0.48), residues: 112 loop : -1.72 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 265 HIS 0.006 0.001 HIS K 499 PHE 0.018 0.001 PHE K 240 TYR 0.028 0.002 TYR H 108 ARG 0.006 0.000 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.04872 ( 914) hydrogen bonds : angle 3.47664 ( 2423) covalent geometry : bond 0.00306 (20028) covalent geometry : angle 0.62075 (28253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6953.24 seconds wall clock time: 122 minutes 24.02 seconds (7344.02 seconds total)