Starting phenix.real_space_refine on Wed Nov 19 20:05:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pe5_20323/11_2025/6pe5_20323.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pe5_20323/11_2025/6pe5_20323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pe5_20323/11_2025/6pe5_20323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pe5_20323/11_2025/6pe5_20323.map" model { file = "/net/cci-nas-00/data/ceres_data/6pe5_20323/11_2025/6pe5_20323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pe5_20323/11_2025/6pe5_20323.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 173 5.16 5 C 17925 2.51 5 N 4492 2.21 5 O 5052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27642 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 6142 Classifications: {'peptide': 758} Link IDs: {'PTRANS': 21, 'TRANS': 736} Chain breaks: 2 Chain: "B" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 406 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2802 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 335} Chain: "E" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 554 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "F" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 561 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "G" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1484 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 196} Chain: "H" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1149 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "I" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "J" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "K" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "L" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "M" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "N" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "O" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "P" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1140 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "Q" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2712 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 20, 'TRANS': 348} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "R" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2712 Classifications: {'peptide': 369} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 20, 'TRANS': 348} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 5.91, per 1000 atoms: 0.21 Number of scatterers: 27642 At special positions: 0 Unit cell: (157.29, 170.13, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 173 16.00 O 5052 8.00 N 4492 7.00 C 17925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6642 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 8 sheets defined 69.8% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.791A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 removed outlier: 4.252A pdb=" N LEU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 77 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 128 removed outlier: 4.391A pdb=" N GLU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 4.152A pdb=" N ASP A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.771A pdb=" N LEU A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.512A pdb=" N ARG A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.697A pdb=" N LYS A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.545A pdb=" N PHE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.693A pdb=" N GLN A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.700A pdb=" N THR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 4.091A pdb=" N MET A 422 " --> pdb=" O MET A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 441 removed outlier: 3.780A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 447 removed outlier: 4.018A pdb=" N ILE A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 460 Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.525A pdb=" N TRP A 522 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 523 " --> pdb=" O TRP A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 519 through 523' Processing helix chain 'A' and resid 527 through 552 removed outlier: 3.535A pdb=" N PHE A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 removed outlier: 3.941A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 596 removed outlier: 3.691A pdb=" N ILE A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Proline residue: A 574 - end of helix removed outlier: 3.610A pdb=" N ILE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 602 removed outlier: 3.677A pdb=" N ASP A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 4.025A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.833A pdb=" N VAL A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 650 through 658 removed outlier: 3.623A pdb=" N PHE A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 724 through 732 removed outlier: 3.605A pdb=" N SER A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 754 removed outlier: 3.657A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.809A pdb=" N PHE A 759 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 760 " --> pdb=" O ILE A 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 756 through 760' Processing helix chain 'A' and resid 763 through 784 removed outlier: 4.004A pdb=" N VAL A 767 " --> pdb=" O GLY A 763 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 768 " --> pdb=" O PHE A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 803 removed outlier: 3.535A pdb=" N THR A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 removed outlier: 3.521A pdb=" N ALA A 830 " --> pdb=" O ASP A 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.733A pdb=" N ASN B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'D' and resid 6 through 22 removed outlier: 7.072A pdb=" N PHE D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 35 Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.626A pdb=" N LEU D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.697A pdb=" N LEU D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 116 removed outlier: 3.556A pdb=" N LYS D 93 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR D 102 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.545A pdb=" N THR D 138 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 140 " --> pdb=" O PRO D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.819A pdb=" N PHE D 162 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 200 removed outlier: 3.707A pdb=" N GLU D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 198 " --> pdb=" O ASN D 194 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 227 removed outlier: 3.736A pdb=" N CYS D 207 " --> pdb=" O PRO D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 251 through 258 removed outlier: 4.009A pdb=" N HIS D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.523A pdb=" N VAL D 265 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 299 removed outlier: 3.856A pdb=" N HIS D 287 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE D 288 " --> pdb=" O LEU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 306 through 332 removed outlier: 4.339A pdb=" N TRP D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.758A pdb=" N ARG D 337 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 334 through 338' Processing helix chain 'E' and resid 4 through 23 removed outlier: 3.713A pdb=" N ILE E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 53 removed outlier: 4.041A pdb=" N ILE E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 42 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP E 48 " --> pdb=" O MET E 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 33 removed outlier: 3.664A pdb=" N CYS F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU F 16 " --> pdb=" O CYS F 12 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 73 removed outlier: 3.724A pdb=" N ALA F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN F 72 " --> pdb=" O PHE F 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 40 removed outlier: 3.754A pdb=" N GLY G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 53 removed outlier: 3.584A pdb=" N PHE G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 51 " --> pdb=" O PHE G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 90 removed outlier: 3.936A pdb=" N TRP G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 97 removed outlier: 3.578A pdb=" N ILE G 96 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR G 97 " --> pdb=" O PRO G 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 93 through 97' Processing helix chain 'G' and resid 101 through 122 removed outlier: 3.834A pdb=" N CYS G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL G 110 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA G 111 " --> pdb=" O CYS G 107 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 135 through 177 removed outlier: 3.537A pdb=" N ASP G 177 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 192 removed outlier: 3.925A pdb=" N VAL G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 206 removed outlier: 4.151A pdb=" N LEU G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 48 removed outlier: 4.012A pdb=" N GLY H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.601A pdb=" N LEU H 55 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE H 56 " --> pdb=" O PRO H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52 through 56' Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.683A pdb=" N ILE H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 126 removed outlier: 3.588A pdb=" N GLY H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 163 removed outlier: 3.658A pdb=" N VAL H 146 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU H 147 " --> pdb=" O PHE H 143 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY H 148 " --> pdb=" O SER H 144 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER H 163 " --> pdb=" O ASN H 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 43 removed outlier: 4.153A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 50 Processing helix chain 'I' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 152 removed outlier: 4.451A pdb=" N GLY I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU I 139 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 43 removed outlier: 4.154A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 54 through 76 removed outlier: 4.154A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 120 removed outlier: 3.503A pdb=" N GLY J 87 " --> pdb=" O ALA J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 124 No H-bonds generated for 'chain 'J' and resid 122 through 124' Processing helix chain 'J' and resid 125 through 152 removed outlier: 4.430A pdb=" N LEU J 139 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 43 removed outlier: 4.154A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 50 Processing helix chain 'K' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 125 through 152 removed outlier: 4.430A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY K 140 " --> pdb=" O ALA K 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 43 removed outlier: 4.153A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 50 Processing helix chain 'L' and resid 54 through 76 removed outlier: 4.154A pdb=" N ILE L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 120 removed outlier: 3.503A pdb=" N GLY L 87 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 124 No H-bonds generated for 'chain 'L' and resid 122 through 124' Processing helix chain 'L' and resid 125 through 152 removed outlier: 4.430A pdb=" N LEU L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 43 removed outlier: 4.154A pdb=" N GLY M 13 " --> pdb=" O ALA M 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 50 Processing helix chain 'M' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE M 63 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY M 87 " --> pdb=" O ALA M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 152 removed outlier: 4.451A pdb=" N GLY M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU M 139 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 43 removed outlier: 4.154A pdb=" N GLY N 13 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE N 21 " --> pdb=" O CYS N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 50 Processing helix chain 'N' and resid 54 through 76 removed outlier: 4.154A pdb=" N ILE N 63 " --> pdb=" O MET N 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA N 64 " --> pdb=" O ALA N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 120 removed outlier: 3.503A pdb=" N GLY N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 152 removed outlier: 4.452A pdb=" N GLY N 128 " --> pdb=" O ARG N 124 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU N 139 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY N 140 " --> pdb=" O ALA N 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 43 removed outlier: 4.153A pdb=" N GLY O 13 " --> pdb=" O ALA O 9 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE O 21 " --> pdb=" O CYS O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 50 Processing helix chain 'O' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE O 63 " --> pdb=" O MET O 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA O 64 " --> pdb=" O ALA O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 152 removed outlier: 4.451A pdb=" N GLY O 128 " --> pdb=" O ARG O 124 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU O 139 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY O 140 " --> pdb=" O ALA O 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 43 removed outlier: 4.153A pdb=" N GLY P 13 " --> pdb=" O ALA P 9 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE P 21 " --> pdb=" O CYS P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 50 Processing helix chain 'P' and resid 54 through 76 removed outlier: 4.153A pdb=" N ILE P 63 " --> pdb=" O MET P 59 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 120 removed outlier: 3.504A pdb=" N GLY P 87 " --> pdb=" O ALA P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 152 removed outlier: 4.451A pdb=" N GLY P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU P 139 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY P 140 " --> pdb=" O ALA P 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 65 Processing helix chain 'Q' and resid 75 through 81 removed outlier: 4.227A pdb=" N LYS Q 81 " --> pdb=" O GLN Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 93 removed outlier: 3.821A pdb=" N ALA Q 91 " --> pdb=" O THR Q 87 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 117 Processing helix chain 'Q' and resid 125 through 134 Processing helix chain 'Q' and resid 140 through 147 removed outlier: 3.727A pdb=" N GLN Q 144 " --> pdb=" O ASP Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 211 removed outlier: 3.775A pdb=" N GLU Q 195 " --> pdb=" O ALA Q 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Q 198 " --> pdb=" O ARG Q 194 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN Q 202 " --> pdb=" O LYS Q 198 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA Q 207 " --> pdb=" O GLY Q 203 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS Q 209 " --> pdb=" O ALA Q 205 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 253 removed outlier: 3.781A pdb=" N MET Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Q 230 " --> pdb=" O SER Q 226 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU Q 233 " --> pdb=" O MET Q 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Q 240 " --> pdb=" O GLY Q 236 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA Q 245 " --> pdb=" O SER Q 241 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY Q 247 " --> pdb=" O GLU Q 243 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 310 Processing helix chain 'Q' and resid 337 through 348 removed outlier: 3.868A pdb=" N ALA Q 346 " --> pdb=" O ARG Q 342 " (cutoff:3.500A) Processing helix chain 'Q' and resid 365 through 380 removed outlier: 3.526A pdb=" N ALA Q 370 " --> pdb=" O GLN Q 366 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA Q 371 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU Q 375 " --> pdb=" O ALA Q 371 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET Q 378 " --> pdb=" O THR Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 419 Processing helix chain 'Q' and resid 425 through 434 removed outlier: 3.928A pdb=" N LYS Q 434 " --> pdb=" O ARG Q 430 " (cutoff:3.500A) Processing helix chain 'Q' and resid 439 through 444 Processing helix chain 'Q' and resid 466 through 476 removed outlier: 3.704A pdb=" N LEU Q 473 " --> pdb=" O GLN Q 469 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP Q 474 " --> pdb=" O LEU Q 470 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU Q 476 " --> pdb=" O ALA Q 472 " (cutoff:3.500A) Processing helix chain 'Q' and resid 480 through 488 Processing helix chain 'R' and resid 61 through 65 Processing helix chain 'R' and resid 75 through 81 removed outlier: 4.227A pdb=" N LYS R 81 " --> pdb=" O GLN R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 93 removed outlier: 3.822A pdb=" N ALA R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 125 through 134 Processing helix chain 'R' and resid 140 through 147 removed outlier: 3.727A pdb=" N GLN R 144 " --> pdb=" O ASP R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 211 removed outlier: 3.775A pdb=" N GLU R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS R 198 " --> pdb=" O ARG R 194 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN R 202 " --> pdb=" O LYS R 198 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS R 209 " --> pdb=" O ALA R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 253 removed outlier: 3.781A pdb=" N MET R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN R 230 " --> pdb=" O SER R 226 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU R 233 " --> pdb=" O MET R 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA R 245 " --> pdb=" O SER R 241 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY R 247 " --> pdb=" O GLU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 310 Processing helix chain 'R' and resid 337 through 348 removed outlier: 3.868A pdb=" N ALA R 346 " --> pdb=" O ARG R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 380 removed outlier: 3.525A pdb=" N ALA R 370 " --> pdb=" O GLN R 366 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA R 371 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU R 375 " --> pdb=" O ALA R 371 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET R 378 " --> pdb=" O THR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 Processing helix chain 'R' and resid 425 through 434 removed outlier: 3.928A pdb=" N LYS R 434 " --> pdb=" O ARG R 430 " (cutoff:3.500A) Processing helix chain 'R' and resid 439 through 444 Processing helix chain 'R' and resid 466 through 476 removed outlier: 3.704A pdb=" N LEU R 473 " --> pdb=" O GLN R 469 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP R 474 " --> pdb=" O LEU R 470 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU R 476 " --> pdb=" O ALA R 472 " (cutoff:3.500A) Processing helix chain 'R' and resid 480 through 488 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.317A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 214 through 217 removed outlier: 3.655A pdb=" N VAL A 216 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 189 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR A 188 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 323 through 326 removed outlier: 3.543A pdb=" N GLY Q 329 " --> pdb=" O ASN Q 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 446 through 448 Processing sheet with id=AA6, first strand: chain 'R' and resid 323 through 326 removed outlier: 3.543A pdb=" N GLY R 329 " --> pdb=" O ASN R 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 446 through 448 Processing sheet with id=AA8, first strand: chain 'R' and resid 451 through 452 removed outlier: 3.555A pdb=" N GLY R 455 " --> pdb=" O ALA R 452 " (cutoff:3.500A) 1805 hydrogen bonds defined for protein. 5313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7613 1.34 - 1.46: 5128 1.46 - 1.57: 15150 1.57 - 1.69: 0 1.69 - 1.81: 280 Bond restraints: 28171 Sorted by residual: bond pdb=" CG1 ILE A 245 " pdb=" CD1 ILE A 245 " ideal model delta sigma weight residual 1.513 1.358 0.155 3.90e-02 6.57e+02 1.58e+01 bond pdb=" N ILE D 245 " pdb=" CA ILE D 245 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" CB TRP G 77 " pdb=" CG TRP G 77 " ideal model delta sigma weight residual 1.498 1.392 0.106 3.10e-02 1.04e+03 1.16e+01 bond pdb=" N GLN J 122 " pdb=" CA GLN J 122 " ideal model delta sigma weight residual 1.463 1.489 -0.027 8.80e-03 1.29e+04 9.09e+00 bond pdb=" N GLN L 122 " pdb=" CA GLN L 122 " ideal model delta sigma weight residual 1.463 1.489 -0.026 8.80e-03 1.29e+04 9.05e+00 ... (remaining 28166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 37673 3.42 - 6.83: 434 6.83 - 10.25: 91 10.25 - 13.66: 32 13.66 - 17.08: 1 Bond angle restraints: 38231 Sorted by residual: angle pdb=" C ILE O 54 " pdb=" N VAL O 55 " pdb=" CA VAL O 55 " ideal model delta sigma weight residual 120.24 126.21 -5.97 6.30e-01 2.52e+00 8.97e+01 angle pdb=" C ILE P 54 " pdb=" N VAL P 55 " pdb=" CA VAL P 55 " ideal model delta sigma weight residual 120.24 126.20 -5.96 6.30e-01 2.52e+00 8.95e+01 angle pdb=" C ILE L 54 " pdb=" N VAL L 55 " pdb=" CA VAL L 55 " ideal model delta sigma weight residual 120.24 126.17 -5.93 6.30e-01 2.52e+00 8.85e+01 angle pdb=" C ILE J 54 " pdb=" N VAL J 55 " pdb=" CA VAL J 55 " ideal model delta sigma weight residual 120.24 126.16 -5.92 6.30e-01 2.52e+00 8.84e+01 angle pdb=" C ILE N 54 " pdb=" N VAL N 55 " pdb=" CA VAL N 55 " ideal model delta sigma weight residual 120.24 126.16 -5.92 6.30e-01 2.52e+00 8.83e+01 ... (remaining 38226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 15688 15.22 - 30.45: 657 30.45 - 45.67: 199 45.67 - 60.90: 24 60.90 - 76.12: 26 Dihedral angle restraints: 16594 sinusoidal: 6167 harmonic: 10427 Sorted by residual: dihedral pdb=" CA ASN F 43 " pdb=" C ASN F 43 " pdb=" N ASP F 44 " pdb=" CA ASP F 44 " ideal model delta harmonic sigma weight residual -180.00 -136.83 -43.17 0 5.00e+00 4.00e-02 7.46e+01 dihedral pdb=" CD ARG R 456 " pdb=" NE ARG R 456 " pdb=" CZ ARG R 456 " pdb=" NH1 ARG R 456 " ideal model delta sinusoidal sigma weight residual 0.00 -75.58 75.58 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CD ARG J 124 " pdb=" NE ARG J 124 " pdb=" CZ ARG J 124 " pdb=" NH1 ARG J 124 " ideal model delta sinusoidal sigma weight residual 0.00 75.49 -75.49 1 1.00e+01 1.00e-02 7.19e+01 ... (remaining 16591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3624 0.066 - 0.132: 771 0.132 - 0.197: 97 0.197 - 0.263: 18 0.263 - 0.329: 4 Chirality restraints: 4514 Sorted by residual: chirality pdb=" CA PHE D 133 " pdb=" N PHE D 133 " pdb=" C PHE D 133 " pdb=" CB PHE D 133 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE A 482 " pdb=" CA ILE A 482 " pdb=" CG1 ILE A 482 " pdb=" CG2 ILE A 482 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL R 120 " pdb=" CA VAL R 120 " pdb=" CG1 VAL R 120 " pdb=" CG2 VAL R 120 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4511 not shown) Planarity restraints: 4807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 456 " -1.063 9.50e-02 1.11e+02 4.76e-01 1.37e+02 pdb=" NE ARG R 456 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG R 456 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG R 456 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG R 456 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 124 " 1.062 9.50e-02 1.11e+02 4.76e-01 1.37e+02 pdb=" NE ARG J 124 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG J 124 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 124 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 124 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 46 " -0.884 9.50e-02 1.11e+02 3.96e-01 9.52e+01 pdb=" NE ARG J 46 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG J 46 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 46 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG J 46 " -0.024 2.00e-02 2.50e+03 ... (remaining 4804 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 447 2.69 - 3.24: 26449 3.24 - 3.80: 42160 3.80 - 4.35: 56897 4.35 - 4.90: 94429 Nonbonded interactions: 220382 Sorted by model distance: nonbonded pdb=" O TYR D 97 " pdb=" OH TYR D 188 " model vdw 2.138 3.040 nonbonded pdb=" OG SER F 41 " pdb=" OD1 ASN F 43 " model vdw 2.237 3.040 nonbonded pdb=" O MET Q 345 " pdb=" OH TYR Q 486 " model vdw 2.253 3.040 nonbonded pdb=" O MET R 345 " pdb=" OH TYR R 486 " model vdw 2.254 3.040 nonbonded pdb=" O THR A 383 " pdb=" OG1 THR A 387 " model vdw 2.293 3.040 ... (remaining 220377 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 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' } 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 individual isotropic 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: 1.510 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: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.810 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.007 0.155 28171 Z= 0.312 Angle : 1.071 17.080 38231 Z= 0.573 Chirality : 0.056 0.329 4514 Planarity : 0.015 0.476 4807 Dihedral : 10.653 76.121 9952 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.41 % Favored : 93.37 % Rotamer: Outliers : 0.45 % Allowed : 3.37 % Favored : 96.19 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.11), residues: 3620 helix: -1.78 (0.08), residues: 2426 sheet: -1.67 (0.56), residues: 72 loop : -3.15 (0.15), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 315 TYR 0.034 0.002 TYR G 57 PHE 0.053 0.004 PHE F 65 TRP 0.030 0.003 TRP D 312 HIS 0.021 0.002 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00719 (28171) covalent geometry : angle 1.07079 (38231) hydrogen bonds : bond 0.18111 ( 1803) hydrogen bonds : angle 6.28400 ( 5313) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 667 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 563 ASN cc_start: 0.7722 (t0) cc_final: 0.7441 (t0) REVERT: E 17 MET cc_start: 0.7362 (ptm) cc_final: 0.7152 (ptp) REVERT: E 20 LEU cc_start: 0.9064 (tm) cc_final: 0.8593 (tp) REVERT: G 27 ILE cc_start: 0.9183 (mt) cc_final: 0.8943 (mt) REVERT: G 47 PHE cc_start: 0.8324 (t80) cc_final: 0.8061 (t80) REVERT: G 205 MET cc_start: 0.9163 (mtp) cc_final: 0.8921 (mtp) REVERT: L 42 THR cc_start: 0.8059 (m) cc_final: 0.7682 (m) REVERT: Q 206 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: R 318 VAL cc_start: 0.8810 (t) cc_final: 0.8564 (m) REVERT: R 407 GLU cc_start: 0.6669 (pt0) cc_final: 0.6468 (pt0) outliers start: 13 outliers final: 6 residues processed: 677 average time/residue: 0.2029 time to fit residues: 210.5843 Evaluate side-chains 400 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 393 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 46 ARG Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain Q residue 206 GLU Chi-restraints excluded: chain Q residue 454 ASN Chi-restraints excluded: chain R residue 454 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 123 GLN A 630 GLN A 796 HIS D 7 ASN D 244 ASN E 55 GLN G 132 ASN J 122 GLN K 53 ASN L 121 GLN Q 217 GLN Q 411 ASN ** Q 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 469 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.133269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100699 restraints weight = 34636.161| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.31 r_work: 0.2898 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28171 Z= 0.139 Angle : 0.620 13.306 38231 Z= 0.317 Chirality : 0.040 0.197 4514 Planarity : 0.005 0.055 4807 Dihedral : 5.122 55.924 3923 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.06 % Allowed : 9.68 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3620 helix: 0.38 (0.10), residues: 2432 sheet: -1.19 (0.60), residues: 76 loop : -2.50 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 124 TYR 0.015 0.001 TYR A 285 PHE 0.032 0.001 PHE D 133 TRP 0.016 0.001 TRP E 48 HIS 0.003 0.001 HIS A 381 Details of bonding type rmsd covalent geometry : bond 0.00271 (28171) covalent geometry : angle 0.62034 (38231) hydrogen bonds : bond 0.06003 ( 1803) hydrogen bonds : angle 3.98623 ( 5313) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 446 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 344 ASP cc_start: 0.7351 (p0) cc_final: 0.6744 (p0) REVERT: A 453 GLU cc_start: 0.6325 (tp30) cc_final: 0.5719 (tp30) REVERT: A 487 MET cc_start: 0.8116 (mmt) cc_final: 0.7844 (mmt) REVERT: A 563 ASN cc_start: 0.8283 (t0) cc_final: 0.7981 (t0) REVERT: D 122 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7082 (tm-30) REVERT: D 178 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7652 (tt0) REVERT: D 236 ASP cc_start: 0.8425 (m-30) cc_final: 0.8191 (m-30) REVERT: D 262 PHE cc_start: 0.9055 (t80) cc_final: 0.8798 (t80) REVERT: E 20 LEU cc_start: 0.8660 (tm) cc_final: 0.8322 (tp) REVERT: G 27 ILE cc_start: 0.9243 (mt) cc_final: 0.8991 (mt) REVERT: J 156 GLN cc_start: 0.7907 (mm110) cc_final: 0.7683 (tt0) REVERT: K 144 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9032 (tp) REVERT: M 1 MET cc_start: 0.6637 (ttp) cc_final: 0.6417 (ttp) REVERT: N 77 SER cc_start: 0.9054 (t) cc_final: 0.8841 (t) REVERT: O 68 LEU cc_start: 0.9408 (tm) cc_final: 0.9206 (tp) REVERT: P 137 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: Q 194 ARG cc_start: 0.7374 (mmp-170) cc_final: 0.6758 (ttm-80) REVERT: R 111 LEU cc_start: 0.7689 (mp) cc_final: 0.7247 (mp) REVERT: R 227 MET cc_start: 0.8584 (mmm) cc_final: 0.8283 (mmm) outliers start: 60 outliers final: 23 residues processed: 485 average time/residue: 0.1896 time to fit residues: 145.1649 Evaluate side-chains 392 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 367 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 190 PHE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 451 ASP Chi-restraints excluded: chain Q residue 454 ASN Chi-restraints excluded: chain R residue 235 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 80 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 34 optimal weight: 0.0040 chunk 284 optimal weight: 40.0000 chunk 339 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** Q 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.086818 restraints weight = 34790.770| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.32 r_work: 0.2694 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 28171 Z= 0.251 Angle : 0.722 16.325 38231 Z= 0.365 Chirality : 0.045 0.237 4514 Planarity : 0.005 0.052 4807 Dihedral : 5.042 59.207 3910 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.48 % Rotamer: Outliers : 2.99 % Allowed : 11.16 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3620 helix: 0.92 (0.10), residues: 2431 sheet: -1.04 (0.57), residues: 81 loop : -2.32 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 124 TYR 0.025 0.002 TYR L 8 PHE 0.039 0.002 PHE D 133 TRP 0.022 0.002 TRP G 77 HIS 0.006 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00617 (28171) covalent geometry : angle 0.72242 (38231) hydrogen bonds : bond 0.08005 ( 1803) hydrogen bonds : angle 4.02486 ( 5313) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 378 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7905 (pp20) cc_final: 0.7658 (pp20) REVERT: A 98 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7259 (tp) REVERT: A 344 ASP cc_start: 0.7374 (p0) cc_final: 0.6908 (p0) REVERT: A 453 GLU cc_start: 0.6564 (tp30) cc_final: 0.6096 (tp30) REVERT: A 487 MET cc_start: 0.8032 (mmt) cc_final: 0.7474 (mmt) REVERT: A 556 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9004 (tp) REVERT: B 246 ASN cc_start: 0.9011 (m110) cc_final: 0.8755 (m-40) REVERT: D 122 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7466 (tm-30) REVERT: D 150 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: D 178 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7687 (tt0) REVERT: D 236 ASP cc_start: 0.8453 (m-30) cc_final: 0.7472 (t0) REVERT: D 262 PHE cc_start: 0.9126 (t80) cc_final: 0.8813 (t80) REVERT: E 20 LEU cc_start: 0.8733 (tm) cc_final: 0.8508 (tp) REVERT: G 27 ILE cc_start: 0.9306 (mt) cc_final: 0.9079 (mt) REVERT: G 108 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8567 (tm-30) REVERT: G 133 MET cc_start: 0.8718 (tpt) cc_final: 0.8307 (tpt) REVERT: H 118 MET cc_start: 0.9244 (mmm) cc_final: 0.8980 (mmm) REVERT: I 81 LYS cc_start: 0.9108 (mttm) cc_final: 0.8764 (mtpp) REVERT: L 5 CYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8417 (p) REVERT: L 8 TYR cc_start: 0.5648 (m-80) cc_final: 0.5264 (p90) REVERT: L 91 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9146 (tp) REVERT: N 68 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9211 (tp) REVERT: O 68 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9269 (tp) REVERT: P 137 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: R 326 ASN cc_start: 0.7911 (p0) cc_final: 0.7680 (p0) outliers start: 87 outliers final: 53 residues processed: 443 average time/residue: 0.1880 time to fit residues: 131.4808 Evaluate side-chains 401 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 340 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 5 CYS Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 440 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 294 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 292 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 348 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN D 116 HIS Q 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.089395 restraints weight = 34252.124| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.30 r_work: 0.2722 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28171 Z= 0.161 Angle : 0.599 17.688 38231 Z= 0.304 Chirality : 0.041 0.189 4514 Planarity : 0.004 0.053 4807 Dihedral : 4.715 59.825 3908 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.51 % Allowed : 13.05 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3620 helix: 1.48 (0.11), residues: 2420 sheet: -0.99 (0.56), residues: 79 loop : -2.16 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 124 TYR 0.014 0.001 TYR L 8 PHE 0.034 0.001 PHE D 133 TRP 0.013 0.001 TRP A 647 HIS 0.005 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00369 (28171) covalent geometry : angle 0.59869 (38231) hydrogen bonds : bond 0.06457 ( 1803) hydrogen bonds : angle 3.76546 ( 5313) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 368 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7908 (pp20) cc_final: 0.7661 (pp20) REVERT: A 98 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6600 (pt) REVERT: A 344 ASP cc_start: 0.7421 (p0) cc_final: 0.6917 (p0) REVERT: A 453 GLU cc_start: 0.6623 (tp30) cc_final: 0.6115 (tp30) REVERT: A 487 MET cc_start: 0.8039 (mmt) cc_final: 0.7513 (mmt) REVERT: A 556 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8979 (tp) REVERT: A 804 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: B 246 ASN cc_start: 0.8957 (m110) cc_final: 0.8693 (m-40) REVERT: D 122 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7408 (tm-30) REVERT: D 150 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: D 236 ASP cc_start: 0.8419 (m-30) cc_final: 0.7409 (t0) REVERT: D 262 PHE cc_start: 0.9061 (t80) cc_final: 0.8702 (t80) REVERT: G 27 ILE cc_start: 0.9272 (mt) cc_final: 0.9028 (mt) REVERT: G 108 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8521 (tt0) REVERT: G 133 MET cc_start: 0.8624 (tpt) cc_final: 0.8355 (tpt) REVERT: H 118 MET cc_start: 0.9123 (mmm) cc_final: 0.8796 (mmm) REVERT: I 81 LYS cc_start: 0.9081 (mttm) cc_final: 0.8752 (mtpp) REVERT: J 68 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8945 (tp) REVERT: L 5 CYS cc_start: 0.8761 (m) cc_final: 0.8327 (p) REVERT: O 68 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9234 (tp) REVERT: P 137 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7695 (mt-10) outliers start: 73 outliers final: 40 residues processed: 423 average time/residue: 0.1859 time to fit residues: 123.7941 Evaluate side-chains 385 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 338 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 166 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.087205 restraints weight = 34157.641| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.35 r_work: 0.2673 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28171 Z= 0.209 Angle : 0.649 18.663 38231 Z= 0.327 Chirality : 0.043 0.208 4514 Planarity : 0.004 0.051 4807 Dihedral : 4.900 82.511 3908 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.88 % Allowed : 13.12 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3620 helix: 1.55 (0.11), residues: 2421 sheet: -0.94 (0.57), residues: 81 loop : -2.12 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 124 TYR 0.020 0.002 TYR D 345 PHE 0.035 0.002 PHE D 133 TRP 0.017 0.002 TRP G 77 HIS 0.005 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00507 (28171) covalent geometry : angle 0.64913 (38231) hydrogen bonds : bond 0.07219 ( 1803) hydrogen bonds : angle 3.84101 ( 5313) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 349 time to evaluate : 1.071 Fit side-chains REVERT: A 85 GLU cc_start: 0.7974 (pp20) cc_final: 0.7732 (pp20) REVERT: A 98 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.6779 (pt) REVERT: A 344 ASP cc_start: 0.7583 (p0) cc_final: 0.7155 (p0) REVERT: A 453 GLU cc_start: 0.6775 (tp30) cc_final: 0.6208 (tp30) REVERT: A 556 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9000 (tp) REVERT: A 804 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: B 246 ASN cc_start: 0.8998 (m110) cc_final: 0.8776 (m-40) REVERT: D 122 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7508 (tm-30) REVERT: D 150 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: D 178 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7686 (tt0) REVERT: D 236 ASP cc_start: 0.8367 (m-30) cc_final: 0.7479 (t0) REVERT: D 262 PHE cc_start: 0.9151 (t80) cc_final: 0.8741 (t80) REVERT: E 68 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.7222 (mtt180) REVERT: F 56 TYR cc_start: 0.8207 (t80) cc_final: 0.7986 (t80) REVERT: G 27 ILE cc_start: 0.9322 (mt) cc_final: 0.9086 (mt) REVERT: G 108 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8530 (tt0) REVERT: G 133 MET cc_start: 0.8772 (tpt) cc_final: 0.8513 (tpt) REVERT: H 118 MET cc_start: 0.9207 (mmm) cc_final: 0.8872 (mmm) REVERT: I 81 LYS cc_start: 0.9139 (mttm) cc_final: 0.8817 (mtpp) REVERT: L 5 CYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8531 (p) REVERT: O 68 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9252 (tp) REVERT: R 111 LEU cc_start: 0.7739 (mp) cc_final: 0.7111 (mp) REVERT: R 368 MET cc_start: 0.7978 (ptp) cc_final: 0.7750 (ptp) outliers start: 84 outliers final: 60 residues processed: 416 average time/residue: 0.1899 time to fit residues: 124.8018 Evaluate side-chains 404 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 338 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 5 CYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 300 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 263 optimal weight: 0.5980 chunk 246 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN E 55 GLN R 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.084803 restraints weight = 34309.700| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.28 r_work: 0.2630 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 28171 Z= 0.268 Angle : 0.701 19.586 38231 Z= 0.353 Chirality : 0.045 0.222 4514 Planarity : 0.005 0.050 4807 Dihedral : 5.030 69.772 3908 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.43 % Allowed : 12.91 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3620 helix: 1.45 (0.11), residues: 2416 sheet: -0.67 (0.60), residues: 74 loop : -2.15 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 124 TYR 0.028 0.002 TYR D 345 PHE 0.039 0.002 PHE D 133 TRP 0.019 0.002 TRP G 77 HIS 0.005 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00667 (28171) covalent geometry : angle 0.70098 (38231) hydrogen bonds : bond 0.07966 ( 1803) hydrogen bonds : angle 3.96752 ( 5313) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 331 time to evaluate : 1.102 Fit side-chains REVERT: A 85 GLU cc_start: 0.7991 (pp20) cc_final: 0.7754 (pp20) REVERT: A 98 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6425 (pt) REVERT: A 112 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7620 (ptp90) REVERT: A 453 GLU cc_start: 0.6795 (tp30) cc_final: 0.6222 (tp30) REVERT: A 487 MET cc_start: 0.7832 (mmm) cc_final: 0.7398 (tpp) REVERT: A 556 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8945 (tp) REVERT: A 804 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: B 246 ASN cc_start: 0.9009 (m110) cc_final: 0.8767 (m-40) REVERT: D 122 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 150 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: D 178 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7630 (tt0) REVERT: D 236 ASP cc_start: 0.8339 (m-30) cc_final: 0.7457 (t0) REVERT: D 262 PHE cc_start: 0.9128 (t80) cc_final: 0.8718 (t80) REVERT: D 266 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8531 (ttt180) REVERT: E 20 LEU cc_start: 0.8829 (tp) cc_final: 0.8595 (tt) REVERT: E 54 CYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8367 (p) REVERT: E 68 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.7215 (mtt180) REVERT: G 27 ILE cc_start: 0.9307 (mt) cc_final: 0.9079 (mt) REVERT: G 108 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8638 (tt0) REVERT: G 133 MET cc_start: 0.8812 (tpt) cc_final: 0.8544 (tpt) REVERT: I 81 LYS cc_start: 0.9149 (mttm) cc_final: 0.8824 (mtpp) REVERT: L 5 CYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8597 (p) REVERT: M 50 LEU cc_start: 0.9118 (tp) cc_final: 0.8832 (tt) REVERT: O 68 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9282 (tp) outliers start: 100 outliers final: 68 residues processed: 409 average time/residue: 0.1844 time to fit residues: 119.6852 Evaluate side-chains 401 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 325 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 5 CYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 308 ASP Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 114 VAL Chi-restraints excluded: chain R residue 324 ILE Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 10 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 321 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 277 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN D 81 ASN P 121 GLN R 202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.088469 restraints weight = 33934.088| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.32 r_work: 0.2707 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28171 Z= 0.155 Angle : 0.591 19.579 38231 Z= 0.299 Chirality : 0.040 0.180 4514 Planarity : 0.004 0.050 4807 Dihedral : 4.698 74.211 3908 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.85 % Allowed : 13.56 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 3620 helix: 1.81 (0.11), residues: 2419 sheet: -0.65 (0.59), residues: 77 loop : -2.09 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 124 TYR 0.014 0.001 TYR D 345 PHE 0.033 0.001 PHE D 133 TRP 0.010 0.001 TRP D 310 HIS 0.005 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00355 (28171) covalent geometry : angle 0.59098 (38231) hydrogen bonds : bond 0.06354 ( 1803) hydrogen bonds : angle 3.71918 ( 5313) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 357 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7922 (pp20) cc_final: 0.7717 (pp20) REVERT: A 98 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6634 (pt) REVERT: A 112 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7668 (ptp90) REVERT: A 453 GLU cc_start: 0.6773 (tp30) cc_final: 0.6226 (tp30) REVERT: A 487 MET cc_start: 0.7928 (mmm) cc_final: 0.7546 (tpp) REVERT: A 556 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9052 (tp) REVERT: A 804 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: B 246 ASN cc_start: 0.8941 (m110) cc_final: 0.8696 (m-40) REVERT: D 122 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7530 (tm-30) REVERT: D 150 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: D 236 ASP cc_start: 0.8297 (m-30) cc_final: 0.7453 (t0) REVERT: D 262 PHE cc_start: 0.9178 (t80) cc_final: 0.8787 (t80) REVERT: E 20 LEU cc_start: 0.8877 (tp) cc_final: 0.8670 (tt) REVERT: E 54 CYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8450 (p) REVERT: E 68 ARG cc_start: 0.7569 (mtt-85) cc_final: 0.7301 (mtt180) REVERT: F 32 ASN cc_start: 0.8492 (t0) cc_final: 0.8211 (t0) REVERT: G 27 ILE cc_start: 0.9339 (mt) cc_final: 0.9086 (mt) REVERT: G 108 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8490 (tt0) REVERT: G 133 MET cc_start: 0.8730 (tpt) cc_final: 0.8506 (tpt) REVERT: I 1 MET cc_start: 0.7433 (ttm) cc_final: 0.7148 (ttp) REVERT: I 81 LYS cc_start: 0.9133 (mttm) cc_final: 0.8820 (mtpp) REVERT: J 68 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8957 (tp) REVERT: L 5 CYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8689 (p) REVERT: M 50 LEU cc_start: 0.9072 (tp) cc_final: 0.8784 (tt) REVERT: O 68 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9242 (tp) REVERT: P 137 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: R 311 LYS cc_start: 0.6397 (mmtm) cc_final: 0.5951 (pttt) outliers start: 83 outliers final: 59 residues processed: 418 average time/residue: 0.1862 time to fit residues: 123.5039 Evaluate side-chains 404 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 335 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain L residue 5 CYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 324 ILE Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 344 optimal weight: 0.3980 chunk 206 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 325 optimal weight: 0.0870 chunk 304 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 0.0470 chunk 330 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.091952 restraints weight = 34082.875| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.33 r_work: 0.2797 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28171 Z= 0.118 Angle : 0.550 19.070 38231 Z= 0.277 Chirality : 0.038 0.162 4514 Planarity : 0.004 0.050 4807 Dihedral : 4.371 79.699 3905 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.44 % Allowed : 14.08 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3620 helix: 2.18 (0.11), residues: 2426 sheet: -0.71 (0.58), residues: 77 loop : -2.02 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 124 TYR 0.010 0.001 TYR A 535 PHE 0.030 0.001 PHE D 133 TRP 0.010 0.001 TRP E 33 HIS 0.005 0.001 HIS A 796 Details of bonding type rmsd covalent geometry : bond 0.00231 (28171) covalent geometry : angle 0.54968 (38231) hydrogen bonds : bond 0.05006 ( 1803) hydrogen bonds : angle 3.48975 ( 5313) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 370 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7836 (pp20) cc_final: 0.7541 (pp20) REVERT: A 98 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7001 (pt) REVERT: A 112 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7573 (ptp90) REVERT: A 344 ASP cc_start: 0.7552 (p0) cc_final: 0.7169 (p0) REVERT: A 453 GLU cc_start: 0.6714 (tp30) cc_final: 0.6281 (tp30) REVERT: A 487 MET cc_start: 0.7859 (mmm) cc_final: 0.7601 (tpp) REVERT: A 764 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6282 (t80) REVERT: A 804 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8540 (mp0) REVERT: B 246 ASN cc_start: 0.8821 (m110) cc_final: 0.8600 (m-40) REVERT: D 105 ASP cc_start: 0.8410 (m-30) cc_final: 0.8026 (m-30) REVERT: D 150 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: D 236 ASP cc_start: 0.8237 (m-30) cc_final: 0.7376 (t0) REVERT: D 262 PHE cc_start: 0.9111 (t80) cc_final: 0.8717 (t80) REVERT: E 20 LEU cc_start: 0.8757 (tp) cc_final: 0.8547 (tt) REVERT: E 68 ARG cc_start: 0.7224 (mtt-85) cc_final: 0.6918 (mtt180) REVERT: F 32 ASN cc_start: 0.8330 (t0) cc_final: 0.8053 (t0) REVERT: G 27 ILE cc_start: 0.9231 (mt) cc_final: 0.8936 (mt) REVERT: G 108 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8365 (tt0) REVERT: G 133 MET cc_start: 0.8712 (tpt) cc_final: 0.8474 (tpt) REVERT: H 65 MET cc_start: 0.9256 (tpp) cc_final: 0.8939 (mtp) REVERT: I 81 LYS cc_start: 0.8993 (mttm) cc_final: 0.8597 (mtpp) REVERT: J 68 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8913 (tp) REVERT: L 5 CYS cc_start: 0.8767 (m) cc_final: 0.8534 (p) REVERT: L 68 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9175 (tp) REVERT: P 137 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: Q 315 MET cc_start: 0.5903 (ppp) cc_final: 0.4233 (ptp) REVERT: R 311 LYS cc_start: 0.6305 (mmtm) cc_final: 0.5894 (pttt) outliers start: 71 outliers final: 49 residues processed: 420 average time/residue: 0.1833 time to fit residues: 122.9562 Evaluate side-chains 406 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 349 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 190 PHE Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 291 optimal weight: 0.0370 chunk 89 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 318 optimal weight: 40.0000 chunk 203 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 275 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN Q 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.086022 restraints weight = 34594.969| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.28 r_work: 0.2693 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28171 Z= 0.195 Angle : 0.625 19.041 38231 Z= 0.314 Chirality : 0.042 0.191 4514 Planarity : 0.004 0.050 4807 Dihedral : 4.510 74.218 3905 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.37 % Allowed : 14.18 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.14), residues: 3620 helix: 1.99 (0.11), residues: 2420 sheet: -0.67 (0.59), residues: 77 loop : -2.01 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 124 TYR 0.018 0.001 TYR D 345 PHE 0.035 0.002 PHE D 133 TRP 0.015 0.001 TRP G 77 HIS 0.004 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00472 (28171) covalent geometry : angle 0.62494 (38231) hydrogen bonds : bond 0.06698 ( 1803) hydrogen bonds : angle 3.69657 ( 5313) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 339 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7879 (pp20) cc_final: 0.7571 (pp20) REVERT: A 98 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6597 (pt) REVERT: A 112 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7645 (ptp90) REVERT: A 453 GLU cc_start: 0.6768 (tp30) cc_final: 0.6123 (tp30) REVERT: A 487 MET cc_start: 0.7982 (mmm) cc_final: 0.7616 (tpp) REVERT: A 804 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: B 246 ASN cc_start: 0.8928 (m110) cc_final: 0.8685 (m-40) REVERT: D 150 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: D 236 ASP cc_start: 0.8270 (m-30) cc_final: 0.7435 (t0) REVERT: D 237 LEU cc_start: 0.8691 (mp) cc_final: 0.8423 (mp) REVERT: D 262 PHE cc_start: 0.9154 (t80) cc_final: 0.8732 (t80) REVERT: E 20 LEU cc_start: 0.8868 (tp) cc_final: 0.8629 (tt) REVERT: E 68 ARG cc_start: 0.7496 (mtt-85) cc_final: 0.7241 (mtt180) REVERT: F 32 ASN cc_start: 0.8519 (t0) cc_final: 0.8268 (t0) REVERT: G 27 ILE cc_start: 0.9300 (mt) cc_final: 0.9042 (mt) REVERT: G 108 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8552 (tt0) REVERT: G 133 MET cc_start: 0.8732 (tpt) cc_final: 0.8471 (tpt) REVERT: I 81 LYS cc_start: 0.9127 (mttm) cc_final: 0.8821 (mtpp) REVERT: L 5 CYS cc_start: 0.8887 (m) cc_final: 0.8627 (p) REVERT: M 50 LEU cc_start: 0.9097 (tp) cc_final: 0.8802 (tt) REVERT: N 77 SER cc_start: 0.9136 (t) cc_final: 0.8847 (p) REVERT: O 68 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9240 (tp) REVERT: P 52 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8669 (ttmt) REVERT: P 137 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: Q 315 MET cc_start: 0.5914 (ppp) cc_final: 0.4456 (ptp) REVERT: R 311 LYS cc_start: 0.6367 (mmtm) cc_final: 0.5946 (pttt) outliers start: 69 outliers final: 53 residues processed: 390 average time/residue: 0.1887 time to fit residues: 116.7558 Evaluate side-chains 389 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 330 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain R residue 324 ILE Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 169 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 317 optimal weight: 40.0000 chunk 259 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 255 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN D 287 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.085960 restraints weight = 34557.941| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.27 r_work: 0.2696 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28171 Z= 0.182 Angle : 0.616 19.595 38231 Z= 0.310 Chirality : 0.041 0.190 4514 Planarity : 0.004 0.050 4807 Dihedral : 4.546 74.589 3905 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.16 % Allowed : 14.56 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.14), residues: 3620 helix: 1.97 (0.11), residues: 2418 sheet: -0.67 (0.59), residues: 77 loop : -1.97 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 124 TYR 0.021 0.001 TYR F 56 PHE 0.034 0.002 PHE D 133 TRP 0.012 0.001 TRP G 77 HIS 0.004 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00435 (28171) covalent geometry : angle 0.61580 (38231) hydrogen bonds : bond 0.06642 ( 1803) hydrogen bonds : angle 3.70504 ( 5313) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 339 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7803 (pp20) cc_final: 0.7512 (pp20) REVERT: A 98 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6524 (pt) REVERT: A 112 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7671 (ptp90) REVERT: A 453 GLU cc_start: 0.6754 (tp30) cc_final: 0.6138 (tp30) REVERT: A 487 MET cc_start: 0.7936 (mmm) cc_final: 0.7635 (tpp) REVERT: A 804 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: B 246 ASN cc_start: 0.8934 (m110) cc_final: 0.8696 (m-40) REVERT: D 150 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: D 236 ASP cc_start: 0.8236 (m-30) cc_final: 0.7434 (t0) REVERT: D 237 LEU cc_start: 0.8705 (mp) cc_final: 0.8455 (mp) REVERT: D 262 PHE cc_start: 0.9138 (t80) cc_final: 0.8744 (t80) REVERT: E 20 LEU cc_start: 0.8872 (tp) cc_final: 0.8656 (tt) REVERT: F 32 ASN cc_start: 0.8497 (t0) cc_final: 0.8244 (t0) REVERT: G 27 ILE cc_start: 0.9324 (mt) cc_final: 0.9071 (mt) REVERT: G 108 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8577 (tt0) REVERT: G 133 MET cc_start: 0.8734 (tpt) cc_final: 0.8405 (tpt) REVERT: I 81 LYS cc_start: 0.9090 (mttm) cc_final: 0.8802 (mtpp) REVERT: J 68 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8913 (tp) REVERT: L 5 CYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8609 (p) REVERT: M 50 LEU cc_start: 0.9094 (tp) cc_final: 0.8792 (tt) REVERT: N 77 SER cc_start: 0.9108 (t) cc_final: 0.8818 (p) REVERT: O 68 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9263 (tp) REVERT: P 52 LYS cc_start: 0.8978 (ttmm) cc_final: 0.8684 (ttmt) REVERT: P 137 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: Q 315 MET cc_start: 0.5753 (ppp) cc_final: 0.4432 (ptp) REVERT: R 311 LYS cc_start: 0.6467 (mmtm) cc_final: 0.6029 (pttt) outliers start: 63 outliers final: 54 residues processed: 386 average time/residue: 0.1853 time to fit residues: 113.5988 Evaluate side-chains 399 residues out of total 2982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 337 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain D residue 9 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain F residue 13 CYS Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain H residue 125 ARG Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 5 CYS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 42 THR Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 137 GLU Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain Q residue 114 VAL Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain R residue 324 ILE Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 164 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 233 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 322 optimal weight: 30.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.085482 restraints weight = 34546.156| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.30 r_work: 0.2662 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 28171 Z= 0.228 Angle : 0.659 19.822 38231 Z= 0.331 Chirality : 0.043 0.207 4514 Planarity : 0.004 0.050 4807 Dihedral : 4.659 71.278 3905 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.51 % Allowed : 14.32 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.14), residues: 3620 helix: 1.83 (0.11), residues: 2423 sheet: -0.64 (0.60), residues: 77 loop : -2.00 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 124 TYR 0.022 0.002 TYR D 345 PHE 0.036 0.002 PHE D 133 TRP 0.016 0.002 TRP G 77 HIS 0.006 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00564 (28171) covalent geometry : angle 0.65884 (38231) hydrogen bonds : bond 0.07288 ( 1803) hydrogen bonds : angle 3.80673 ( 5313) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7378.48 seconds wall clock time: 126 minutes 41.68 seconds (7601.68 seconds total)