Starting phenix.real_space_refine on Sun Nov 19 01:19:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe4_20322/11_2023/6pe4_20322_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe4_20322/11_2023/6pe4_20322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe4_20322/11_2023/6pe4_20322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe4_20322/11_2023/6pe4_20322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe4_20322/11_2023/6pe4_20322_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pe4_20322/11_2023/6pe4_20322_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 156 5.16 5 C 16229 2.51 5 N 4021 2.21 5 O 4508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "H TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "I ARG 46": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I GLU 137": "OE1" <-> "OE2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 124": "NH1" <-> "NH2" Residue "J ARG 153": "NH1" <-> "NH2" Residue "K ARG 46": "NH1" <-> "NH2" Residue "K ARG 117": "NH1" <-> "NH2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K ARG 153": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 117": "NH1" <-> "NH2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "M ARG 153": "NH1" <-> "NH2" Residue "N ARG 117": "NH1" <-> "NH2" Residue "N ARG 153": "NH1" <-> "NH2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 124": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P ARG 46": "NH1" <-> "NH2" Residue "P ARG 153": "NH1" <-> "NH2" Residue "Q ARG 108": "NH1" <-> "NH2" Residue "Q ARG 224": "NH1" <-> "NH2" Residue "Q ARG 456": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 24914 Number of models: 1 Model: "" Number of chains: 16 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: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1132 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "P" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1132 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} 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: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 12.93, per 1000 atoms: 0.52 Number of scatterers: 24914 At special positions: 0 Unit cell: (150.87, 145.52, 129.47, 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 156 16.00 O 4508 8.00 N 4021 7.00 C 16229 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 - 3.50 Amino acid : False - 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: 9.60 Conformation dependent library (CDL) restraints added in 4.8 seconds 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5954 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 6 sheets defined 70.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 4.223A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 76 Processing helix chain 'A' and resid 104 through 133 removed outlier: 4.145A pdb=" N GLU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.596A pdb=" N PHE A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.535A pdb=" N LEU A 153 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.777A pdb=" N LYS A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.560A pdb=" N ASN A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 289 removed outlier: 3.762A pdb=" N ASP A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.564A pdb=" N LYS A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 321 removed outlier: 3.841A pdb=" N TRP A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.511A pdb=" N SER A 326 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.876A pdb=" N LEU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 Processing helix chain 'A' and resid 410 through 423 removed outlier: 3.516A pdb=" N PHE A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 3.519A pdb=" N PHE A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 422 " --> pdb=" O MET A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 441 removed outlier: 3.544A pdb=" N PHE A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.904A pdb=" N HIS A 523 " --> pdb=" O TRP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 552 removed outlier: 4.121A pdb=" N ASN A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 removed outlier: 3.870A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 removed outlier: 3.556A pdb=" N ILE A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 removed outlier: 3.599A pdb=" N MET A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 595 removed outlier: 3.503A pdb=" N TRP A 594 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 595 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.689A pdb=" N VAL A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 4.365A 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: 3.561A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 723 Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 755 removed outlier: 3.558A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.645A pdb=" N GLY A 760 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 761 " --> pdb=" O ALA A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 784 removed outlier: 4.078A pdb=" N PHE A 768 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 803 removed outlier: 4.040A pdb=" N SER A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 799 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 832 removed outlier: 3.715A pdb=" N ALA A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 246 removed outlier: 3.516A pdb=" N CYS B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.679A 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 2 through 7 removed outlier: 3.535A pdb=" N PHE D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 7' Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 26 through 35 removed outlier: 3.598A pdb=" N TYR D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.603A pdb=" N LEU D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 85 removed outlier: 3.570A pdb=" N GLN D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 116 removed outlier: 3.817A pdb=" N LYS D 93 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR D 102 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.717A 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: 3.539A pdb=" N SER D 140 " --> pdb=" O PRO D 137 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D 141 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 removed outlier: 3.578A pdb=" N GLU D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.597A pdb=" N PHE D 162 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 200 removed outlier: 3.599A pdb=" N GLU D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 226 removed outlier: 3.824A 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 257 Processing helix chain 'D' and resid 261 through 270 removed outlier: 3.704A pdb=" N VAL D 265 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 299 removed outlier: 3.810A pdb=" N PHE D 288 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 331 removed outlier: 3.799A pdb=" N TRP D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 23 removed outlier: 3.701A pdb=" N VAL E 8 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE E 21 " --> pdb=" O MET E 17 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 53 removed outlier: 4.063A pdb=" N ILE E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP E 48 " --> pdb=" O MET E 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 33 removed outlier: 3.893A pdb=" N LEU F 16 " --> pdb=" O CYS F 12 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE F 23 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.959A pdb=" N ALA F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 40 Processing helix chain 'G' and resid 41 through 45 removed outlier: 3.778A pdb=" N ILE G 45 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 removed outlier: 3.502A pdb=" N PHE G 50 " --> pdb=" O ASN G 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 52 " --> pdb=" O GLY G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 89 removed outlier: 3.895A pdb=" N TRP G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 100 removed outlier: 4.259A pdb=" N LYS G 99 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 122 removed outlier: 3.608A pdb=" N CYS G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL G 110 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA G 111 " --> pdb=" O CYS G 107 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY G 114 " --> pdb=" O VAL G 110 " (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 Processing helix chain 'G' and resid 180 through 206 removed outlier: 4.072A pdb=" N VAL G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU G 188 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE G 193 " --> pdb=" O ILE G 189 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU G 194 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 196 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 48 removed outlier: 3.766A pdb=" N GLY H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.672A pdb=" N LEU H 55 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 3.674A 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 81 removed outlier: 3.764A pdb=" N ILE H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU H 69 " --> pdb=" O MET H 65 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA H 70 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 126 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'H' and resid 133 through 144 Processing helix chain 'H' and resid 145 through 163 removed outlier: 3.685A pdb=" N LEU H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER H 163 " --> pdb=" O ASN H 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 43 removed outlier: 4.147A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA I 20 " --> pdb=" O GLY I 16 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE I 23 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.563A pdb=" N LEU I 49 " --> pdb=" O ARG I 46 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 46 through 50' Processing helix chain 'I' and resid 54 through 76 removed outlier: 3.617A pdb=" N ILE I 62 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE I 63 " --> pdb=" O MET I 59 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 120 removed outlier: 3.779A pdb=" N VAL I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER I 120 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 136 removed outlier: 3.851A pdb=" N PHE I 135 " --> pdb=" O LEU I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 152 removed outlier: 3.558A pdb=" N LEU I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 43 removed outlier: 4.409A pdb=" N PHE J 12 " --> pdb=" O TYR J 8 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER J 19 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.570A pdb=" N LEU J 49 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU J 50 " --> pdb=" O PRO J 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 46 through 50' Processing helix chain 'J' and resid 54 through 76 removed outlier: 3.520A pdb=" N ALA J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE J 62 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 119 removed outlier: 3.620A pdb=" N GLY J 87 " --> pdb=" O ALA J 83 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 152 removed outlier: 4.419A pdb=" N GLY J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU J 139 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU J 141 " --> pdb=" O GLU J 137 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 39 removed outlier: 4.344A pdb=" N PHE K 12 " --> pdb=" O TYR K 8 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY K 16 " --> pdb=" O PHE K 12 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA K 20 " --> pdb=" O GLY K 16 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 76 removed outlier: 3.752A pdb=" N GLY K 67 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 119 removed outlier: 3.619A pdb=" N ALA K 114 " --> pdb=" O ILE K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 121 No H-bonds generated for 'chain 'K' and resid 120 through 121' Processing helix chain 'K' and resid 122 through 123 No H-bonds generated for 'chain 'K' and resid 122 through 123' Processing helix chain 'K' and resid 124 through 153 removed outlier: 3.859A pdb=" N GLY K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY K 140 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG K 153 " --> pdb=" O LEU K 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 41 removed outlier: 4.136A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA L 20 " --> pdb=" O GLY L 16 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 75 removed outlier: 4.005A pdb=" N ILE L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 78 No H-bonds generated for 'chain 'L' and resid 76 through 78' Processing helix chain 'L' and resid 83 through 119 removed outlier: 3.881A pdb=" N VAL L 97 " --> pdb=" O ALA L 93 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA L 114 " --> pdb=" O ILE L 110 " (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: 3.585A pdb=" N PHE L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU L 141 " --> pdb=" O GLU L 137 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 43 removed outlier: 4.047A pdb=" N PHE M 12 " --> pdb=" O TYR M 8 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY M 13 " --> pdb=" O ALA M 9 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA M 20 " --> pdb=" O GLY M 16 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE M 23 " --> pdb=" O SER M 19 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL M 37 " --> pdb=" O ALA M 33 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 50 removed outlier: 4.044A pdb=" N LEU M 49 " --> pdb=" O ARG M 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 46 through 50' Processing helix chain 'M' and resid 54 through 76 removed outlier: 4.014A pdb=" N ILE M 63 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY M 67 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR M 76 " --> pdb=" O VAL M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 119 removed outlier: 3.748A pdb=" N SER M 100 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 124 No H-bonds generated for 'chain 'M' and resid 122 through 124' Processing helix chain 'M' and resid 125 through 151 removed outlier: 3.899A pdb=" N PHE M 135 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU M 139 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN M 151 " --> pdb=" O ALA M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 154 No H-bonds generated for 'chain 'M' and resid 152 through 154' Processing helix chain 'N' and resid 9 through 43 removed outlier: 4.106A pdb=" N GLY N 13 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA N 20 " --> pdb=" O GLY N 16 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE N 21 " --> pdb=" O CYS N 17 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE N 23 " --> pdb=" O SER N 19 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR N 24 " --> pdb=" O ALA N 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER N 35 " --> pdb=" O GLY N 31 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL N 37 " --> pdb=" O ALA N 33 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 50 removed outlier: 3.717A pdb=" N LEU N 49 " --> pdb=" O ARG N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 76 removed outlier: 4.065A pdb=" N ILE N 63 " --> pdb=" O MET N 59 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA N 64 " --> pdb=" O ALA N 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE N 65 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY N 67 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR N 76 " --> pdb=" O VAL N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 119 removed outlier: 3.985A pdb=" N ALA N 114 " --> pdb=" O ILE N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 154 removed outlier: 4.530A pdb=" N GLY N 128 " --> pdb=" O ARG N 124 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU N 139 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY N 140 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU N 141 " --> pdb=" O GLU N 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA N 154 " --> pdb=" O LEU N 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 43 removed outlier: 4.359A pdb=" N GLY O 13 " --> pdb=" O ALA O 9 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA O 14 " --> pdb=" O PRO O 10 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE O 21 " --> pdb=" O CYS O 17 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR O 30 " --> pdb=" O LEU O 26 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY O 38 " --> pdb=" O LYS O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 50 removed outlier: 3.717A pdb=" N LEU O 50 " --> pdb=" O PRO O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 61 Processing helix chain 'O' and resid 62 through 76 Processing helix chain 'O' and resid 83 through 119 removed outlier: 3.768A pdb=" N VAL O 97 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 124 No H-bonds generated for 'chain 'O' and resid 122 through 124' Processing helix chain 'O' and resid 125 through 152 removed outlier: 3.655A pdb=" N PHE O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU O 139 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY O 140 " --> pdb=" O ALA O 136 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU O 141 " --> pdb=" O GLU O 137 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 43 removed outlier: 3.663A pdb=" N GLY P 16 " --> pdb=" O PHE P 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA P 20 " --> pdb=" O GLY P 16 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE P 21 " --> pdb=" O CYS P 17 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR P 24 " --> pdb=" O ALA P 20 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR P 30 " --> pdb=" O LEU P 26 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY P 38 " --> pdb=" O LYS P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 45 No H-bonds generated for 'chain 'P' and resid 44 through 45' Processing helix chain 'P' and resid 46 through 50 removed outlier: 3.671A pdb=" N LEU P 49 " --> pdb=" O ARG P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 61 through 76 removed outlier: 3.820A pdb=" N ILE P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 118 removed outlier: 3.747A pdb=" N ALA P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA P 104 " --> pdb=" O SER P 100 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE P 106 " --> pdb=" O LEU P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 136 removed outlier: 4.179A pdb=" N GLY P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET P 129 " --> pdb=" O LEU P 125 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE P 135 " --> pdb=" O LEU P 131 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 152 removed outlier: 3.547A pdb=" N LEU P 141 " --> pdb=" O GLU P 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 93 removed outlier: 3.597A pdb=" N TYR Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 117 removed outlier: 3.609A pdb=" N GLU Q 112 " --> pdb=" O ARG Q 108 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER Q 115 " --> pdb=" O LEU Q 111 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU Q 116 " --> pdb=" O GLU Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 134 Processing helix chain 'Q' and resid 140 through 150 removed outlier: 3.546A pdb=" N GLN Q 144 " --> pdb=" O ASP Q 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER Q 146 " --> pdb=" O ARG Q 142 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU Q 148 " --> pdb=" O GLN Q 144 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN Q 150 " --> pdb=" O SER Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 211 removed outlier: 3.687A pdb=" N ALA Q 205 " --> pdb=" O VAL Q 201 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU Q 206 " --> pdb=" O ASN Q 202 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA Q 207 " --> pdb=" O GLY Q 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 230 removed outlier: 3.868A pdb=" N MET Q 229 " --> pdb=" O LEU Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 253 Processing helix chain 'Q' and resid 302 through 308 Processing helix chain 'Q' and resid 309 through 312 Processing helix chain 'Q' and resid 337 through 348 removed outlier: 3.908A pdb=" N ALA Q 346 " --> pdb=" O ARG Q 342 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR Q 347 " --> pdb=" O ALA Q 343 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 380 Processing helix chain 'Q' and resid 407 through 421 removed outlier: 3.671A pdb=" N GLU Q 420 " --> pdb=" O LYS Q 416 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP Q 421 " --> pdb=" O LEU Q 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 434 removed outlier: 3.806A pdb=" N LYS Q 434 " --> pdb=" O ARG Q 430 " (cutoff:3.500A) Processing helix chain 'Q' and resid 466 through 470 Processing helix chain 'Q' and resid 471 through 476 Processing helix chain 'Q' and resid 480 through 490 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: 4.243A 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: 3.561A pdb=" N VAL A 216 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.362A 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 325 Processing sheet with id=AA5, first strand: chain 'Q' and resid 446 through 448 Processing sheet with id=AA6, first strand: chain 'Q' and resid 451 through 452 removed outlier: 3.692A pdb=" N GLY Q 455 " --> pdb=" O ALA Q 452 " (cutoff:3.500A) 1526 hydrogen bonds defined for protein. 4506 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: 8.37 Time building geometry restraints manager: 10.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6700 1.33 - 1.46: 5103 1.46 - 1.58: 13353 1.58 - 1.70: 1 1.70 - 1.82: 246 Bond restraints: 25403 Sorted by residual: bond pdb=" N GLU H 145 " pdb=" CA GLU H 145 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 6.92e+00 bond pdb=" N GLU I 137 " pdb=" CA GLU I 137 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.28e-02 6.10e+03 6.42e+00 bond pdb=" CB VAL H 105 " pdb=" CG2 VAL H 105 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.34e+00 bond pdb=" N LYS D 163 " pdb=" CA LYS D 163 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.24e-02 6.50e+03 5.87e+00 bond pdb=" N ARG K 46 " pdb=" CA ARG K 46 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.41e-02 5.03e+03 5.51e+00 ... (remaining 25398 not shown) Histogram of bond angle deviations from ideal: 96.18 - 103.87: 313 103.87 - 111.56: 10410 111.56 - 119.25: 10434 119.25 - 126.95: 13069 126.95 - 134.64: 257 Bond angle restraints: 34483 Sorted by residual: angle pdb=" C PHE Q 134 " pdb=" N ASP Q 135 " pdb=" CA ASP Q 135 " ideal model delta sigma weight residual 121.54 132.75 -11.21 1.91e+00 2.74e-01 3.44e+01 angle pdb=" CA LEU A 649 " pdb=" CB LEU A 649 " pdb=" CG LEU A 649 " ideal model delta sigma weight residual 116.30 134.64 -18.34 3.50e+00 8.16e-02 2.75e+01 angle pdb=" C LEU Q 105 " pdb=" N THR Q 106 " pdb=" CA THR Q 106 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C LEU E 53 " pdb=" N CYS E 54 " pdb=" CA CYS E 54 " ideal model delta sigma weight residual 121.54 131.12 -9.58 1.91e+00 2.74e-01 2.52e+01 angle pdb=" CA LEU K 49 " pdb=" CB LEU K 49 " pdb=" CG LEU K 49 " ideal model delta sigma weight residual 116.30 133.34 -17.04 3.50e+00 8.16e-02 2.37e+01 ... (remaining 34478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 14010 15.80 - 31.60: 684 31.60 - 47.40: 156 47.40 - 63.20: 12 63.20 - 79.00: 17 Dihedral angle restraints: 14879 sinusoidal: 5517 harmonic: 9362 Sorted by residual: dihedral pdb=" CA PRO D 201 " pdb=" C PRO D 201 " pdb=" N GLU D 202 " pdb=" CA GLU D 202 " ideal model delta harmonic sigma weight residual -180.00 -152.53 -27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLY A 452 " pdb=" C GLY A 452 " pdb=" N GLU A 453 " pdb=" CA GLU A 453 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ARG N 153 " pdb=" C ARG N 153 " pdb=" N ALA N 154 " pdb=" CA ALA N 154 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 14876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3190 0.066 - 0.132: 774 0.132 - 0.198: 104 0.198 - 0.265: 15 0.265 - 0.331: 3 Chirality restraints: 4086 Sorted by residual: 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 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 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 2.72e+00 chirality pdb=" CB VAL L 55 " pdb=" CA VAL L 55 " pdb=" CG1 VAL L 55 " pdb=" CG2 VAL L 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4083 not shown) Planarity restraints: 4310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 46 " 0.596 9.50e-02 1.11e+02 2.67e-01 4.36e+01 pdb=" NE ARG K 46 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG K 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG K 46 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 46 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 77 " 0.023 2.00e-02 2.50e+03 2.36e-02 1.40e+01 pdb=" CG TRP G 77 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP G 77 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP G 77 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 77 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP G 77 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 77 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 77 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP G 77 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 647 " 0.023 2.00e-02 2.50e+03 2.25e-02 1.26e+01 pdb=" CG TRP A 647 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 647 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 647 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 647 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 647 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 647 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 647 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 647 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 647 " 0.004 2.00e-02 2.50e+03 ... (remaining 4307 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 805 2.71 - 3.26: 24354 3.26 - 3.81: 38547 3.81 - 4.35: 50944 4.35 - 4.90: 85741 Nonbonded interactions: 200391 Sorted by model distance: nonbonded pdb=" O MET H 65 " pdb=" OE2 GLU H 145 " model vdw 2.164 3.040 nonbonded pdb=" O TYR D 249 " pdb=" OG1 THR D 253 " model vdw 2.240 2.440 nonbonded pdb=" NE2 GLN K 122 " pdb=" O GLU Q 420 " model vdw 2.285 2.520 nonbonded pdb=" OG SER H 112 " pdb=" O SER H 144 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR A 31 " pdb=" OE1 GLU A 316 " model vdw 2.307 2.440 ... (remaining 200386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'I' and resid 2 through 159) selection = (chain 'J' and resid 2 through 159) selection = (chain 'K' and resid 2 through 159) selection = (chain 'L' and resid 2 through 159) selection = (chain 'M' and resid 2 through 159) selection = (chain 'N' and resid 2 through 159) selection = chain 'O' selection = chain 'P' } 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: 1.140 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: 6.310 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 64.190 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 25403 Z= 0.515 Angle : 1.100 18.339 34483 Z= 0.557 Chirality : 0.058 0.331 4086 Planarity : 0.008 0.267 4310 Dihedral : 10.556 78.997 8925 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 0.30 % Allowed : 3.80 % Favored : 95.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.11), residues: 3255 helix: -2.33 (0.08), residues: 2237 sheet: -1.70 (0.57), residues: 69 loop : -3.38 (0.16), residues: 949 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 447 time to evaluate : 2.990 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 454 average time/residue: 0.4070 time to fit residues: 279.1682 Evaluate side-chains 306 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 302 time to evaluate : 3.141 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3943 time to fit residues: 6.4060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 287 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 311 GLN A 384 ASN A 563 ASN A 714 HIS D 78 HIS D 125 GLN D 176 ASN D 302 GLN E 30 GLN E 55 GLN F 72 GLN I 121 GLN K 90 GLN L 90 GLN N 82 GLN Q 202 ASN Q 326 ASN Q 366 GLN Q 469 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25403 Z= 0.162 Angle : 0.579 11.440 34483 Z= 0.297 Chirality : 0.039 0.199 4086 Planarity : 0.005 0.045 4310 Dihedral : 4.789 27.176 3512 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 1.59 % Allowed : 7.51 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3255 helix: -0.15 (0.11), residues: 2250 sheet: -0.73 (0.63), residues: 58 loop : -2.91 (0.16), residues: 947 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 365 time to evaluate : 2.816 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 13 residues processed: 400 average time/residue: 0.3558 time to fit residues: 225.3088 Evaluate side-chains 316 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 303 time to evaluate : 2.878 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2214 time to fit residues: 9.2422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 159 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 chunk 311 optimal weight: 4.9990 chunk 256 optimal weight: 0.1980 chunk 285 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN D 125 GLN I 82 GLN O 121 GLN Q 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25403 Z= 0.308 Angle : 0.647 13.367 34483 Z= 0.323 Chirality : 0.043 0.241 4086 Planarity : 0.004 0.042 4310 Dihedral : 4.669 29.702 3512 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.82 % Favored : 95.12 % Rotamer: Outliers : 2.13 % Allowed : 9.94 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3255 helix: 0.57 (0.11), residues: 2255 sheet: -0.24 (0.67), residues: 56 loop : -2.70 (0.17), residues: 944 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 312 time to evaluate : 2.937 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 28 residues processed: 355 average time/residue: 0.3736 time to fit residues: 209.6325 Evaluate side-chains 328 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 300 time to evaluate : 2.877 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2190 time to fit residues: 15.7889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 284 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 289 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 756 GLN D 125 GLN D 176 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN K 90 GLN O 121 GLN Q 129 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25403 Z= 0.313 Angle : 0.625 11.277 34483 Z= 0.314 Chirality : 0.042 0.242 4086 Planarity : 0.004 0.044 4310 Dihedral : 4.605 29.086 3512 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 1.63 % Allowed : 11.31 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3255 helix: 0.89 (0.11), residues: 2248 sheet: -0.19 (0.69), residues: 56 loop : -2.56 (0.17), residues: 951 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 308 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 17 residues processed: 340 average time/residue: 0.3842 time to fit residues: 206.2115 Evaluate side-chains 307 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 290 time to evaluate : 2.785 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2295 time to fit residues: 11.0090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 255 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN D 125 GLN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 25403 Z= 0.304 Angle : 0.608 10.806 34483 Z= 0.308 Chirality : 0.042 0.240 4086 Planarity : 0.004 0.044 4310 Dihedral : 4.539 28.844 3512 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 1.48 % Allowed : 12.71 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 3255 helix: 1.09 (0.11), residues: 2250 sheet: -0.27 (0.70), residues: 56 loop : -2.46 (0.18), residues: 949 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 305 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 17 residues processed: 335 average time/residue: 0.3854 time to fit residues: 203.1651 Evaluate side-chains 307 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 290 time to evaluate : 2.743 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2246 time to fit residues: 10.9275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 103 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 306 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 384 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN L 90 GLN Q 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 25403 Z= 0.306 Angle : 0.607 12.697 34483 Z= 0.307 Chirality : 0.042 0.242 4086 Planarity : 0.004 0.048 4310 Dihedral : 4.506 28.815 3512 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 1.63 % Allowed : 13.02 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3255 helix: 1.19 (0.11), residues: 2248 sheet: -0.30 (0.70), residues: 56 loop : -2.35 (0.18), residues: 951 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 300 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 331 average time/residue: 0.3804 time to fit residues: 198.4453 Evaluate side-chains 308 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 289 time to evaluate : 3.061 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2296 time to fit residues: 11.8919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 295 optimal weight: 0.0030 chunk 34 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 223 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25403 Z= 0.144 Angle : 0.527 13.849 34483 Z= 0.267 Chirality : 0.038 0.194 4086 Planarity : 0.003 0.044 4310 Dihedral : 4.163 26.981 3512 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 0.72 % Allowed : 14.08 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3255 helix: 1.59 (0.11), residues: 2258 sheet: -0.39 (0.73), residues: 54 loop : -2.24 (0.18), residues: 943 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 323 time to evaluate : 3.145 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 337 average time/residue: 0.3827 time to fit residues: 202.7327 Evaluate side-chains 311 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 306 time to evaluate : 2.826 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2491 time to fit residues: 6.0917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN D 176 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25403 Z= 0.283 Angle : 0.595 13.364 34483 Z= 0.300 Chirality : 0.041 0.241 4086 Planarity : 0.004 0.045 4310 Dihedral : 4.288 28.214 3512 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 1.06 % Allowed : 14.27 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3255 helix: 1.54 (0.11), residues: 2250 sheet: -0.25 (0.71), residues: 56 loop : -2.23 (0.18), residues: 949 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 297 time to evaluate : 2.803 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 314 average time/residue: 0.4060 time to fit residues: 199.8929 Evaluate side-chains 306 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 293 time to evaluate : 2.995 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2342 time to fit residues: 10.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 277 optimal weight: 7.9990 chunk 292 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 25403 Z= 0.451 Angle : 0.693 12.889 34483 Z= 0.349 Chirality : 0.046 0.277 4086 Planarity : 0.004 0.055 4310 Dihedral : 4.631 31.312 3512 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 0.57 % Allowed : 14.46 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3255 helix: 1.21 (0.11), residues: 2261 sheet: -0.18 (0.71), residues: 56 loop : -2.31 (0.18), residues: 938 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 288 time to evaluate : 2.943 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 298 average time/residue: 0.3864 time to fit residues: 181.9091 Evaluate side-chains 284 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 278 time to evaluate : 2.999 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2422 time to fit residues: 6.6861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 186 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 315 optimal weight: 0.0040 chunk 290 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 533 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25403 Z= 0.161 Angle : 0.547 12.731 34483 Z= 0.277 Chirality : 0.039 0.198 4086 Planarity : 0.004 0.048 4310 Dihedral : 4.211 27.568 3512 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 0.19 % Allowed : 14.91 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3255 helix: 1.68 (0.11), residues: 2250 sheet: -0.40 (0.72), residues: 54 loop : -2.16 (0.18), residues: 951 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6510 Ramachandran restraints generated. 3255 Oldfield, 0 Emsley, 3255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 301 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 303 average time/residue: 0.4039 time to fit residues: 192.9124 Evaluate side-chains 299 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 298 time to evaluate : 3.037 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2339 time to fit residues: 4.5157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 199 optimal weight: 0.3980 chunk 267 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.079647 restraints weight = 30430.762| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.52 r_work: 0.2594 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 25403 Z= 0.363 Angle : 0.640 13.254 34483 Z= 0.323 Chirality : 0.043 0.259 4086 Planarity : 0.004 0.049 4310 Dihedral : 4.429 29.089 3512 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 0.27 % Allowed : 15.14 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3255 helix: 1.47 (0.11), residues: 2247 sheet: -0.17 (0.71), residues: 56 loop : -2.20 (0.18), residues: 952 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5155.86 seconds wall clock time: 94 minutes 21.19 seconds (5661.19 seconds total)