Starting phenix.real_space_refine on Thu Feb 22 06:49:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpk_21863/02_2024/6wpk_21863.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpk_21863/02_2024/6wpk_21863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpk_21863/02_2024/6wpk_21863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpk_21863/02_2024/6wpk_21863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpk_21863/02_2024/6wpk_21863.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wpk_21863/02_2024/6wpk_21863.pdb" } resolution = 3.3 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= 0.005 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 136 5.16 5 C 20917 2.51 5 N 6072 2.21 5 O 6104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A ARG 697": "NH1" <-> "NH2" Residue "A ARG 702": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B GLU 604": "OE1" <-> "OE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B ARG 697": "NH1" <-> "NH2" Residue "B ARG 702": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C ARG 570": "NH1" <-> "NH2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C ARG 697": "NH1" <-> "NH2" Residue "C ARG 702": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D GLU 544": "OE1" <-> "OE2" Residue "D ARG 570": "NH1" <-> "NH2" Residue "D GLU 604": "OE1" <-> "OE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D ARG 697": "NH1" <-> "NH2" Residue "D ARG 702": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 175": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E GLU 264": "OE1" <-> "OE2" Residue "E GLU 282": "OE1" <-> "OE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "E GLU 544": "OE1" <-> "OE2" Residue "E ARG 570": "NH1" <-> "NH2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E ARG 697": "NH1" <-> "NH2" Residue "E ARG 702": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ARG 175": "NH1" <-> "NH2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F GLU 264": "OE1" <-> "OE2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F ARG 307": "NH1" <-> "NH2" Residue "F GLU 544": "OE1" <-> "OE2" Residue "F ARG 570": "NH1" <-> "NH2" Residue "F GLU 604": "OE1" <-> "OE2" Residue "F GLU 689": "OE1" <-> "OE2" Residue "F ARG 697": "NH1" <-> "NH2" Residue "F ARG 702": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 175": "NH1" <-> "NH2" Residue "G GLU 179": "OE1" <-> "OE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 282": "OE1" <-> "OE2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G GLU 544": "OE1" <-> "OE2" Residue "G ARG 570": "NH1" <-> "NH2" Residue "G GLU 689": "OE1" <-> "OE2" Residue "G ARG 697": "NH1" <-> "NH2" Residue "G ARG 702": "NH1" <-> "NH2" Residue "H ARG 157": "NH1" <-> "NH2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H ARG 162": "NH1" <-> "NH2" Residue "H GLU 174": "OE1" <-> "OE2" Residue "H ARG 175": "NH1" <-> "NH2" Residue "H GLU 179": "OE1" <-> "OE2" Residue "H GLU 196": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H ARG 243": "NH1" <-> "NH2" Residue "H PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 282": "OE1" <-> "OE2" Residue "H GLU 297": "OE1" <-> "OE2" Residue "H ARG 307": "NH1" <-> "NH2" Residue "H GLU 544": "OE1" <-> "OE2" Residue "H ARG 570": "NH1" <-> "NH2" Residue "H GLU 604": "OE1" <-> "OE2" Residue "H GLU 689": "OE1" <-> "OE2" Residue "H ARG 697": "NH1" <-> "NH2" Residue "H ARG 702": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33229 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4157 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4155 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "F" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 4152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4152 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "H" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4153 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 16.60, per 1000 atoms: 0.50 Number of scatterers: 33229 At special positions: 0 Unit cell: (204.37, 204.37, 81.32, 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 136 16.00 O 6104 8.00 N 6072 7.00 C 20917 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: 12.63 Conformation dependent library (CDL) restraints added in 6.4 seconds 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8112 Finding SS restraints... Secondary structure from input PDB file: 324 helices and 16 sheets defined 73.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 52 through 68 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.660A pdb=" N GLN A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.531A pdb=" N LEU A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.609A pdb=" N ARG A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 4.736A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.857A pdb=" N ALA A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.584A pdb=" N LEU A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 236 removed outlier: 3.596A pdb=" N ARG A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.520A pdb=" N ARG A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 265 through 280 removed outlier: 3.986A pdb=" N ASN A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 3.831A pdb=" N SER A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.846A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 359 removed outlier: 3.643A pdb=" N CYS A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.828A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.550A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 459 through 475 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.666A pdb=" N CYS A 482 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP A 483 " --> pdb=" O SER A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 483' Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.814A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.891A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 500' Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.871A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.578A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.549A pdb=" N ALA A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 605 through 614 removed outlier: 3.904A pdb=" N GLY A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 649 removed outlier: 4.258A pdb=" N CYS A 649 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 703 Processing helix chain 'B' and resid 52 through 68 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 105 through 115 removed outlier: 4.364A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.515A pdb=" N GLN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.570A pdb=" N ARG B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 177 through 192 removed outlier: 4.672A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 219 through 236 removed outlier: 3.682A pdb=" N ARG B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.560A pdb=" N ARG B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 265 through 280 removed outlier: 3.974A pdb=" N ASN B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.876A pdb=" N SER B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.810A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 359 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.915A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.510A pdb=" N GLY B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.617A pdb=" N VAL B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 459 through 475 removed outlier: 4.127A pdb=" N GLU B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.760A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.764A pdb=" N ARG B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 500' Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.818A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.736A pdb=" N VAL B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 544 removed outlier: 3.603A pdb=" N ALA B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.843A pdb=" N GLY B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 removed outlier: 3.566A pdb=" N VAL B 644 " --> pdb=" O HIS B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 649 removed outlier: 4.384A pdb=" N CYS B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 703 Processing helix chain 'C' and resid 52 through 68 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 105 through 115 removed outlier: 4.295A pdb=" N GLY C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 135 removed outlier: 3.516A pdb=" N GLN C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.543A pdb=" N LEU C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.606A pdb=" N ARG C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.551A pdb=" N ALA C 181 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.813A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 205 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.611A pdb=" N LEU C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 219 through 236 removed outlier: 3.601A pdb=" N ARG C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 230 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.534A pdb=" N ARG C 243 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 265 through 280 removed outlier: 4.005A pdb=" N ASN C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 removed outlier: 3.807A pdb=" N SER C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 295 Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.868A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 359 removed outlier: 3.669A pdb=" N CYS C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 3.833A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 398 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.555A pdb=" N VAL C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 459 through 475 Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.668A pdb=" N CYS C 482 " --> pdb=" O TYR C 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP C 483 " --> pdb=" O SER C 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 479 through 483' Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.814A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.879A pdb=" N ARG C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.871A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.739A pdb=" N VAL C 518 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 543 removed outlier: 3.559A pdb=" N ALA C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 605 through 614 removed outlier: 3.904A pdb=" N GLY C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 649 removed outlier: 4.218A pdb=" N CYS C 649 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 703 Processing helix chain 'D' and resid 52 through 68 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 105 through 115 removed outlier: 4.348A pdb=" N GLY D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 135 removed outlier: 3.514A pdb=" N GLN D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.574A pdb=" N ARG D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.624A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.880A pdb=" N ALA D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 214 removed outlier: 3.509A pdb=" N LEU D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 219 through 236 removed outlier: 3.506A pdb=" N LEU D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 224 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 230 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.553A pdb=" N ARG D 243 " --> pdb=" O GLN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 265 through 280 removed outlier: 3.972A pdb=" N ASN D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 removed outlier: 3.877A pdb=" N SER D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 295 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 323 through 329 Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.832A pdb=" N LEU D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 359 Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 369 through 380 removed outlier: 3.919A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 398 Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 425 removed outlier: 3.612A pdb=" N VAL D 417 " --> pdb=" O LYS D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 459 through 475 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.761A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.763A pdb=" N ARG D 499 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 496 through 500' Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.847A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.731A pdb=" N VAL D 518 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 544 removed outlier: 3.604A pdb=" N ALA D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 586 Processing helix chain 'D' and resid 605 through 614 removed outlier: 3.841A pdb=" N GLY D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 644 removed outlier: 3.565A pdb=" N VAL D 644 " --> pdb=" O HIS D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 703 Processing helix chain 'E' and resid 52 through 68 Processing helix chain 'E' and resid 78 through 91 Processing helix chain 'E' and resid 105 through 115 removed outlier: 4.292A pdb=" N GLY E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 removed outlier: 3.515A pdb=" N GLN E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 149 removed outlier: 3.520A pdb=" N LEU E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 163 removed outlier: 3.601A pdb=" N ARG E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE E 163 " --> pdb=" O ARG E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 177 through 193 removed outlier: 4.632A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.866A pdb=" N ALA E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 214 removed outlier: 3.624A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 219 through 236 removed outlier: 3.596A pdb=" N ARG E 224 " --> pdb=" O PRO E 220 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 230 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 248 removed outlier: 3.539A pdb=" N ARG E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 258 Proline residue: E 256 - end of helix Processing helix chain 'E' and resid 265 through 280 removed outlier: 3.976A pdb=" N ASN E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 removed outlier: 3.835A pdb=" N SER E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 295 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 323 through 329 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.861A pdb=" N LEU E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 359 removed outlier: 3.642A pdb=" N CYS E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 380 removed outlier: 3.902A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 398 Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 425 removed outlier: 3.554A pdb=" N VAL E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 436 Processing helix chain 'E' and resid 440 through 445 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 459 through 475 Processing helix chain 'E' and resid 479 through 483 removed outlier: 3.667A pdb=" N CYS E 482 " --> pdb=" O TYR E 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP E 483 " --> pdb=" O SER E 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 479 through 483' Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.819A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.864A pdb=" N ARG E 499 " --> pdb=" O PRO E 496 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 496 through 500' Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.868A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.540A pdb=" N VAL E 518 " --> pdb=" O LEU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 543 removed outlier: 3.561A pdb=" N ALA E 541 " --> pdb=" O ARG E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 586 Processing helix chain 'E' and resid 605 through 614 removed outlier: 3.904A pdb=" N GLY E 613 " --> pdb=" O GLN E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 649 removed outlier: 4.252A pdb=" N CYS E 649 " --> pdb=" O THR E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 703 Processing helix chain 'F' and resid 52 through 68 Processing helix chain 'F' and resid 78 through 91 Processing helix chain 'F' and resid 105 through 116 removed outlier: 4.346A pdb=" N GLY F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 135 removed outlier: 3.803A pdb=" N GLN F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'F' and resid 153 through 163 removed outlier: 3.558A pdb=" N ARG F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 177 through 192 removed outlier: 4.720A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.854A pdb=" N ALA F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA F 205 " --> pdb=" O ARG F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 214 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 219 through 236 removed outlier: 3.512A pdb=" N LEU F 223 " --> pdb=" O ASP F 219 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG F 224 " --> pdb=" O PRO F 220 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU F 230 " --> pdb=" O CYS F 226 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 248 removed outlier: 3.559A pdb=" N ARG F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 255 Processing helix chain 'F' and resid 265 through 280 removed outlier: 3.974A pdb=" N ASN F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 290 removed outlier: 3.877A pdb=" N SER F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 295 Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 323 through 329 Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.836A pdb=" N LEU F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 Processing helix chain 'F' and resid 364 through 369 Processing helix chain 'F' and resid 369 through 380 removed outlier: 3.914A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 398 removed outlier: 3.517A pdb=" N GLY F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 425 removed outlier: 3.611A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 429 through 436 Processing helix chain 'F' and resid 440 through 445 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 459 through 475 Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.762A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.764A pdb=" N ARG F 499 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 496 through 500' Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.788A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.733A pdb=" N VAL F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 544 removed outlier: 3.605A pdb=" N ALA F 541 " --> pdb=" O ARG F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 586 Processing helix chain 'F' and resid 605 through 614 removed outlier: 3.833A pdb=" N GLY F 613 " --> pdb=" O GLN F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 644 removed outlier: 3.571A pdb=" N VAL F 644 " --> pdb=" O HIS F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 703 Processing helix chain 'G' and resid 52 through 68 Processing helix chain 'G' and resid 78 through 91 Processing helix chain 'G' and resid 105 through 115 removed outlier: 4.327A pdb=" N GLY G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 135 removed outlier: 3.515A pdb=" N GLN G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA G 135 " --> pdb=" O ARG G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 149 removed outlier: 3.527A pdb=" N LEU G 147 " --> pdb=" O GLN G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 163 removed outlier: 3.592A pdb=" N ARG G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE G 163 " --> pdb=" O ARG G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 177 through 192 removed outlier: 4.779A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.816A pdb=" N ALA G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 214 removed outlier: 3.656A pdb=" N LEU G 212 " --> pdb=" O LEU G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 219 through 236 removed outlier: 3.592A pdb=" N ARG G 224 " --> pdb=" O PRO G 220 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 230 " --> pdb=" O CYS G 226 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 248 removed outlier: 3.534A pdb=" N ARG G 243 " --> pdb=" O GLN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 258 Proline residue: G 256 - end of helix Processing helix chain 'G' and resid 265 through 280 removed outlier: 4.005A pdb=" N ASN G 280 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 290 removed outlier: 3.822A pdb=" N SER G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 295 Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 323 through 329 Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.852A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 359 removed outlier: 3.654A pdb=" N CYS G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 380 removed outlier: 3.855A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 398 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 425 removed outlier: 3.554A pdb=" N VAL G 417 " --> pdb=" O LYS G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 436 Processing helix chain 'G' and resid 440 through 445 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 459 through 475 Processing helix chain 'G' and resid 479 through 483 removed outlier: 3.634A pdb=" N CYS G 482 " --> pdb=" O TYR G 479 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP G 483 " --> pdb=" O SER G 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 479 through 483' Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.813A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP G 495 " --> pdb=" O LEU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 3.864A pdb=" N ARG G 499 " --> pdb=" O PRO G 496 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 496 through 500' Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.868A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.539A pdb=" N VAL G 518 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 544 removed outlier: 3.553A pdb=" N ALA G 541 " --> pdb=" O ARG G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 574 through 586 Processing helix chain 'G' and resid 605 through 614 removed outlier: 3.904A pdb=" N GLY G 613 " --> pdb=" O GLN G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 644 through 649 removed outlier: 4.255A pdb=" N CYS G 649 " --> pdb=" O THR G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 703 Processing helix chain 'H' and resid 52 through 68 Processing helix chain 'H' and resid 78 through 91 Processing helix chain 'H' and resid 105 through 115 removed outlier: 4.350A pdb=" N GLY H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 135 removed outlier: 3.866A pdb=" N GLN H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 149 Processing helix chain 'H' and resid 153 through 163 removed outlier: 3.622A pdb=" N ARG H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 172 Processing helix chain 'H' and resid 177 through 192 removed outlier: 3.546A pdb=" N ALA H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.907A pdb=" N ALA H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 214 Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 219 through 236 removed outlier: 3.680A pdb=" N ARG H 224 " --> pdb=" O PRO H 220 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 230 " --> pdb=" O CYS H 226 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 248 removed outlier: 3.537A pdb=" N ARG H 243 " --> pdb=" O GLN H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 255 Processing helix chain 'H' and resid 265 through 280 removed outlier: 3.920A pdb=" N ASN H 280 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 290 removed outlier: 3.913A pdb=" N SER H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 323 through 329 Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.813A pdb=" N LEU H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 359 Processing helix chain 'H' and resid 364 through 369 Processing helix chain 'H' and resid 369 through 380 removed outlier: 3.914A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 398 removed outlier: 3.513A pdb=" N GLY H 398 " --> pdb=" O LEU H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 425 removed outlier: 3.611A pdb=" N VAL H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 436 Processing helix chain 'H' and resid 440 through 445 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 459 through 475 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.772A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP H 495 " --> pdb=" O LEU H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.764A pdb=" N ARG H 499 " --> pdb=" O PRO H 496 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 496 through 500' Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.796A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.744A pdb=" N VAL H 518 " --> pdb=" O LEU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 544 removed outlier: 3.606A pdb=" N ALA H 541 " --> pdb=" O ARG H 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 586 Processing helix chain 'H' and resid 605 through 614 removed outlier: 3.794A pdb=" N GLY H 613 " --> pdb=" O GLN H 609 " (cutoff:3.500A) Processing helix chain 'H' and resid 639 through 644 removed outlier: 3.569A pdb=" N VAL H 644 " --> pdb=" O HIS H 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 644 through 649 removed outlier: 4.385A pdb=" N CYS H 649 " --> pdb=" O THR H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 687 through 703 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.171A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.171A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE A 656 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 619 " --> pdb=" O ILE A 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE B 656 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 619 " --> pdb=" O ILE B 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.172A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.172A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE C 656 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 619 " --> pdb=" O ILE C 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 566 through 568 removed outlier: 6.434A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 566 through 568 removed outlier: 6.434A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE D 656 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU D 619 " --> pdb=" O ILE D 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 564 through 567 removed outlier: 6.171A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 564 through 567 removed outlier: 6.171A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE E 656 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU E 619 " --> pdb=" O ILE E 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE F 656 " --> pdb=" O PHE F 617 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU F 619 " --> pdb=" O ILE F 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 564 through 567 removed outlier: 6.174A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 564 through 567 removed outlier: 6.174A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE G 656 " --> pdb=" O PHE G 617 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU G 619 " --> pdb=" O ILE G 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 566 through 568 removed outlier: 6.432A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE H 656 " --> pdb=" O PHE H 617 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU H 619 " --> pdb=" O ILE H 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 1722 hydrogen bonds defined for protein. 5022 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: 11.33 Time building geometry restraints manager: 13.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.52: 24631 1.52 - 1.82: 9022 1.82 - 2.11: 0 2.11 - 2.41: 0 2.41 - 2.71: 6 Bond restraints: 33659 Sorted by residual: bond pdb=" C LEU D 116 " pdb=" N ASP D 127 " ideal model delta sigma weight residual 1.328 2.700 -1.373 1.13e-02 7.83e+03 1.48e+04 bond pdb=" C LEU B 116 " pdb=" N ASP B 127 " ideal model delta sigma weight residual 1.332 2.705 -1.373 1.40e-02 5.10e+03 9.61e+03 bond pdb=" C LEU G 116 " pdb=" N ASP G 127 " ideal model delta sigma weight residual 1.332 2.638 -1.306 1.40e-02 5.10e+03 8.70e+03 bond pdb=" C LEU E 116 " pdb=" N ASP E 127 " ideal model delta sigma weight residual 1.332 2.623 -1.290 1.40e-02 5.10e+03 8.49e+03 bond pdb=" C LEU C 116 " pdb=" N ASP C 127 " ideal model delta sigma weight residual 1.332 2.621 -1.289 1.40e-02 5.10e+03 8.47e+03 ... (remaining 33654 not shown) Histogram of bond angle deviations from ideal: 65.33 - 86.94: 6 86.94 - 108.54: 1251 108.54 - 130.15: 43972 130.15 - 151.75: 177 151.75 - 173.36: 12 Bond angle restraints: 45418 Sorted by residual: angle pdb=" O LEU G 116 " pdb=" C LEU G 116 " pdb=" N ASP G 127 " ideal model delta sigma weight residual 123.34 173.36 -50.02 1.37e+00 5.33e-01 1.33e+03 angle pdb=" O LEU C 116 " pdb=" C LEU C 116 " pdb=" N ASP C 127 " ideal model delta sigma weight residual 123.34 173.13 -49.79 1.37e+00 5.33e-01 1.32e+03 angle pdb=" O LEU E 116 " pdb=" C LEU E 116 " pdb=" N ASP E 127 " ideal model delta sigma weight residual 123.34 173.09 -49.75 1.37e+00 5.33e-01 1.32e+03 angle pdb=" CA LEU E 116 " pdb=" C LEU E 116 " pdb=" N ASP E 127 " ideal model delta sigma weight residual 116.50 65.33 51.17 1.44e+00 4.82e-01 1.26e+03 angle pdb=" CA LEU C 116 " pdb=" C LEU C 116 " pdb=" N ASP C 127 " ideal model delta sigma weight residual 116.50 65.45 51.05 1.44e+00 4.82e-01 1.26e+03 ... (remaining 45413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18023 17.98 - 35.95: 1938 35.95 - 53.93: 355 53.93 - 71.91: 81 71.91 - 89.88: 19 Dihedral angle restraints: 20416 sinusoidal: 7938 harmonic: 12478 Sorted by residual: dihedral pdb=" CA LEU F 116 " pdb=" C LEU F 116 " pdb=" N ASP F 127 " pdb=" CA ASP F 127 " ideal model delta harmonic sigma weight residual 180.00 109.54 70.46 0 5.00e+00 4.00e-02 1.99e+02 dihedral pdb=" CA LEU D 116 " pdb=" C LEU D 116 " pdb=" N ASP D 127 " pdb=" CA ASP D 127 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU B 116 " pdb=" C LEU B 116 " pdb=" N ASP B 127 " pdb=" CA ASP B 127 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 20413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4708 0.063 - 0.125: 560 0.125 - 0.188: 19 0.188 - 0.251: 4 0.251 - 0.314: 8 Chirality restraints: 5299 Sorted by residual: chirality pdb=" CA LEU B 303 " pdb=" N LEU B 303 " pdb=" C LEU B 303 " pdb=" CB LEU B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA LEU F 303 " pdb=" N LEU F 303 " pdb=" C LEU F 303 " pdb=" CB LEU F 303 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LEU D 303 " pdb=" N LEU D 303 " pdb=" C LEU D 303 " pdb=" CB LEU D 303 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5296 not shown) Planarity restraints: 5862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 561 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO F 562 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 562 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 562 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 561 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO B 562 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 562 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 562 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 561 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO H 562 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO H 562 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 562 " -0.032 5.00e-02 4.00e+02 ... (remaining 5859 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8778 2.80 - 3.33: 31009 3.33 - 3.85: 50181 3.85 - 4.38: 60932 4.38 - 4.90: 104706 Nonbonded interactions: 255606 Sorted by model distance: nonbonded pdb=" OG SER E 567 " pdb=" OE1 GLU E 642 " model vdw 2.277 2.440 nonbonded pdb=" OG SER A 567 " pdb=" OE1 GLU A 642 " model vdw 2.278 2.440 nonbonded pdb=" OG SER G 567 " pdb=" OE1 GLU G 642 " model vdw 2.278 2.440 nonbonded pdb=" NH2 ARG G 376 " pdb=" OE2 GLU G 472 " model vdw 2.280 2.520 nonbonded pdb=" NH2 ARG E 376 " pdb=" OE2 GLU E 472 " model vdw 2.280 2.520 ... (remaining 255601 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 'A' and (resid 51 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or (resid 89 through 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 544 or (resid 545 and (name N o \ r name CA or name C or name O or name CB or name CG or name SD )) or resid 561 t \ hrough 703)) selection = (chain 'B' and (resid 51 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 544 or (resid 545 and (name N or n \ ame CA or name C or name O or name CB or name CG or name SD )) or resid 561 thro \ ugh 703)) selection = (chain 'C' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) selection = (chain 'D' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) selection = (chain 'E' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) selection = (chain 'F' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) selection = chain 'G' selection = (chain 'H' and (resid 51 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB or name CG or name SD )) or resid 561 through 703)) } 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: 0.850 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: 0.030 Extract box with map and model: 5.940 Check model and map are aligned: 0.540 Set scattering table: 0.250 Process input model: 82.190 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.018 1.373 33659 Z= 1.486 Angle : 1.130 51.168 45418 Z= 0.717 Chirality : 0.043 0.314 5299 Planarity : 0.004 0.058 5862 Dihedral : 15.336 89.883 12304 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.65 % Allowed : 8.51 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.11), residues: 4200 helix: -2.06 (0.09), residues: 2888 sheet: -3.55 (0.32), residues: 104 loop : -3.17 (0.15), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 490 HIS 0.006 0.001 HIS G 236 PHE 0.011 0.001 PHE A 617 TYR 0.008 0.001 TYR C 503 ARG 0.004 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 364 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 641 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5952 (mtmt) REVERT: B 642 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7113 (pt0) REVERT: C 641 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5929 (mtmt) REVERT: D 642 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7106 (pt0) REVERT: E 641 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5968 (mtmt) REVERT: F 217 ARG cc_start: 0.7812 (mmt90) cc_final: 0.7421 (mmm-85) REVERT: G 217 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7937 (mmp80) REVERT: G 641 LYS cc_start: 0.6282 (OUTLIER) cc_final: 0.5943 (mtmt) outliers start: 22 outliers final: 6 residues processed: 386 average time/residue: 0.5506 time to fit residues: 317.3651 Evaluate side-chains 264 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 252 time to evaluate : 3.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain E residue 641 LYS Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain F residue 642 GLU Chi-restraints excluded: chain G residue 641 LYS Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain H residue 642 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 0.9980 chunk 327 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 111 optimal weight: 30.0000 chunk 220 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 252 optimal weight: 0.7980 chunk 392 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN A 239 GLN A 342 GLN A 423 GLN A 436 GLN A 522 GLN A 587 HIS A 640 HIS A 700 GLN B 143 GLN B 239 GLN B 342 GLN B 383 ASN B 423 GLN B 436 GLN B 522 GLN B 587 HIS B 640 HIS B 700 GLN C 143 GLN C 239 GLN C 342 GLN C 423 GLN C 436 GLN C 522 GLN C 587 HIS C 700 GLN D 143 GLN D 239 GLN D 342 GLN D 383 ASN D 423 GLN D 436 GLN D 522 GLN D 587 HIS D 640 HIS D 700 GLN E 143 GLN E 200 GLN E 239 GLN E 342 GLN E 423 GLN E 436 GLN E 522 GLN E 587 HIS E 640 HIS E 700 GLN F 143 GLN F 239 GLN F 342 GLN F 383 ASN F 423 GLN F 436 GLN F 522 GLN F 587 HIS F 640 HIS F 700 GLN G 143 GLN G 200 GLN G 239 GLN G 342 GLN G 423 GLN G 436 GLN G 522 GLN G 587 HIS G 640 HIS G 700 GLN H 143 GLN H 239 GLN H 342 GLN H 383 ASN H 423 GLN H 436 GLN H 522 GLN H 587 HIS H 640 HIS H 700 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33659 Z= 0.165 Angle : 0.582 10.951 45418 Z= 0.282 Chirality : 0.038 0.150 5299 Planarity : 0.004 0.047 5862 Dihedral : 5.216 45.071 4750 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 0.95 % Allowed : 15.11 % Favored : 83.94 % 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: -1.98 (0.13), residues: 4212 helix: -0.67 (0.10), residues: 2934 sheet: -2.23 (0.35), residues: 104 loop : -2.63 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 490 HIS 0.003 0.001 HIS C 236 PHE 0.016 0.001 PHE C 617 TYR 0.008 0.001 TYR D 687 ARG 0.007 0.000 ARG G 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 287 time to evaluate : 3.615 Fit side-chains REVERT: B 399 GLU cc_start: 0.8172 (mp0) cc_final: 0.7864 (tt0) REVERT: B 642 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: C 153 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8137 (m) REVERT: D 642 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7299 (pt0) REVERT: E 153 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8141 (m) REVERT: F 399 GLU cc_start: 0.7793 (tt0) cc_final: 0.7396 (tt0) REVERT: F 642 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: G 217 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7808 (mmp80) REVERT: H 399 GLU cc_start: 0.7795 (tt0) cc_final: 0.7152 (tt0) REVERT: H 642 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7234 (pt0) outliers start: 32 outliers final: 11 residues processed: 305 average time/residue: 0.4563 time to fit residues: 225.6765 Evaluate side-chains 271 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 254 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 642 GLU Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 642 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 326 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 108 optimal weight: 70.0000 chunk 393 optimal weight: 7.9990 chunk 424 optimal weight: 0.9990 chunk 350 optimal weight: 1.9990 chunk 389 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 315 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33659 Z= 0.210 Angle : 0.581 12.602 45418 Z= 0.278 Chirality : 0.038 0.190 5299 Planarity : 0.004 0.044 5862 Dihedral : 4.648 30.937 4722 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.75 % Allowed : 15.76 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.26 (0.13), residues: 4212 helix: -0.12 (0.10), residues: 2928 sheet: -1.66 (0.39), residues: 104 loop : -2.41 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 490 HIS 0.003 0.000 HIS C 236 PHE 0.016 0.001 PHE C 617 TYR 0.009 0.001 TYR F 687 ARG 0.004 0.000 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 250 time to evaluate : 3.921 Fit side-chains REVERT: A 147 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6516 (mm) REVERT: A 656 ILE cc_start: 0.7516 (mt) cc_final: 0.7198 (tt) REVERT: B 330 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 399 GLU cc_start: 0.8219 (mp0) cc_final: 0.7678 (tt0) REVERT: B 489 ASP cc_start: 0.7896 (m-30) cc_final: 0.7428 (m-30) REVERT: C 147 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6336 (mm) REVERT: D 147 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.5987 (mm) REVERT: D 330 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8676 (mp) REVERT: D 489 ASP cc_start: 0.7900 (m-30) cc_final: 0.7424 (m-30) REVERT: E 147 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6228 (mm) REVERT: E 656 ILE cc_start: 0.7411 (mt) cc_final: 0.7028 (tt) REVERT: F 330 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8670 (mp) REVERT: F 489 ASP cc_start: 0.7952 (m-30) cc_final: 0.7487 (m-30) REVERT: G 147 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6410 (mm) REVERT: G 217 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7819 (mmp80) REVERT: H 330 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8679 (mp) REVERT: H 399 GLU cc_start: 0.7503 (tt0) cc_final: 0.6988 (tt0) REVERT: H 489 ASP cc_start: 0.7981 (m-30) cc_final: 0.7505 (m-30) outliers start: 59 outliers final: 19 residues processed: 287 average time/residue: 0.4410 time to fit residues: 207.3464 Evaluate side-chains 267 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 6.9990 chunk 295 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 263 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 417 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 373 optimal weight: 1.9990 chunk 112 optimal weight: 40.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33659 Z= 0.205 Angle : 0.572 12.637 45418 Z= 0.273 Chirality : 0.038 0.190 5299 Planarity : 0.004 0.043 5862 Dihedral : 4.324 15.356 4710 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.35 % Allowed : 16.72 % Favored : 80.93 % 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: -0.78 (0.13), residues: 4212 helix: 0.24 (0.10), residues: 2936 sheet: -1.56 (0.36), residues: 104 loop : -2.21 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 490 HIS 0.003 0.000 HIS E 236 PHE 0.014 0.001 PHE C 617 TYR 0.009 0.001 TYR D 687 ARG 0.003 0.000 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 244 time to evaluate : 4.342 Fit side-chains REVERT: A 147 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6389 (mm) REVERT: A 656 ILE cc_start: 0.7442 (mt) cc_final: 0.7150 (tt) REVERT: B 330 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8694 (mp) REVERT: B 399 GLU cc_start: 0.8196 (mp0) cc_final: 0.7593 (tt0) REVERT: B 489 ASP cc_start: 0.7890 (m-30) cc_final: 0.7432 (m-30) REVERT: C 147 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6395 (mm) REVERT: D 147 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6119 (mm) REVERT: D 489 ASP cc_start: 0.7892 (m-30) cc_final: 0.7419 (m-30) REVERT: E 147 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6364 (mm) REVERT: E 656 ILE cc_start: 0.7602 (mt) cc_final: 0.7387 (tt) REVERT: F 147 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6095 (mm) REVERT: F 489 ASP cc_start: 0.7890 (m-30) cc_final: 0.7435 (m-30) REVERT: G 147 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6301 (mm) REVERT: G 217 ARG cc_start: 0.8070 (mmm160) cc_final: 0.7674 (mmt-90) REVERT: H 330 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8688 (mp) REVERT: H 399 GLU cc_start: 0.7427 (tt0) cc_final: 0.6838 (tt0) REVERT: H 489 ASP cc_start: 0.7976 (m-30) cc_final: 0.7529 (m-30) outliers start: 79 outliers final: 43 residues processed: 301 average time/residue: 0.4560 time to fit residues: 224.5422 Evaluate side-chains 290 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 239 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 383 ASN Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 383 ASN Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Chi-restraints excluded: chain H residue 645 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 4.9990 chunk 237 optimal weight: 0.2980 chunk 6 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 356 optimal weight: 1.9990 chunk 288 optimal weight: 0.6980 chunk 0 optimal weight: 70.0000 chunk 213 optimal weight: 6.9990 chunk 374 optimal weight: 9.9990 chunk 105 optimal weight: 0.0770 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33659 Z= 0.143 Angle : 0.540 12.353 45418 Z= 0.256 Chirality : 0.037 0.185 5299 Planarity : 0.003 0.039 5862 Dihedral : 4.063 14.291 4710 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.99 % Allowed : 17.97 % Favored : 80.04 % 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: -0.24 (0.13), residues: 4212 helix: 0.65 (0.10), residues: 2918 sheet: -1.17 (0.35), residues: 104 loop : -2.04 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 490 HIS 0.002 0.000 HIS G 236 PHE 0.012 0.001 PHE C 617 TYR 0.007 0.001 TYR B 687 ARG 0.002 0.000 ARG G 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 239 time to evaluate : 3.785 Fit side-chains REVERT: B 330 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8668 (mp) REVERT: B 399 GLU cc_start: 0.8134 (mp0) cc_final: 0.7537 (tt0) REVERT: B 489 ASP cc_start: 0.7877 (m-30) cc_final: 0.7573 (m-30) REVERT: C 147 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6391 (mm) REVERT: D 143 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6563 (tt0) REVERT: D 147 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6162 (mm) REVERT: D 330 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8666 (mp) REVERT: D 399 GLU cc_start: 0.8189 (mp0) cc_final: 0.7261 (tt0) REVERT: D 489 ASP cc_start: 0.7898 (m-30) cc_final: 0.7578 (m-30) REVERT: E 147 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6339 (mm) REVERT: E 656 ILE cc_start: 0.7542 (mt) cc_final: 0.7310 (tt) REVERT: F 147 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6172 (mm) REVERT: F 330 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8657 (mp) REVERT: F 489 ASP cc_start: 0.7854 (m-30) cc_final: 0.7491 (m-30) REVERT: G 147 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6297 (mm) REVERT: G 152 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7483 (mm) REVERT: G 217 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7690 (mmt-90) REVERT: H 330 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8671 (mp) REVERT: H 399 GLU cc_start: 0.7328 (tt0) cc_final: 0.6757 (tt0) REVERT: H 489 ASP cc_start: 0.7830 (m-30) cc_final: 0.7458 (m-30) outliers start: 67 outliers final: 34 residues processed: 285 average time/residue: 0.4527 time to fit residues: 210.3148 Evaluate side-chains 266 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 221 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 645 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 3.9990 chunk 376 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 417 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 33659 Z= 0.307 Angle : 0.610 12.977 45418 Z= 0.291 Chirality : 0.040 0.180 5299 Planarity : 0.004 0.045 5862 Dihedral : 4.355 16.303 4710 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.71 % Allowed : 18.05 % Favored : 79.24 % 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: -0.38 (0.13), residues: 4212 helix: 0.53 (0.10), residues: 2942 sheet: -1.46 (0.32), residues: 104 loop : -2.06 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 412 HIS 0.004 0.001 HIS A 236 PHE 0.026 0.001 PHE G 617 TYR 0.010 0.002 TYR B 687 ARG 0.003 0.000 ARG F 463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 232 time to evaluate : 3.841 Fit side-chains REVERT: A 147 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6556 (mm) REVERT: A 152 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7466 (mm) REVERT: B 330 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8746 (mp) REVERT: B 399 GLU cc_start: 0.8105 (mp0) cc_final: 0.7511 (tt0) REVERT: B 489 ASP cc_start: 0.7877 (m-30) cc_final: 0.7367 (m-30) REVERT: C 147 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6535 (mm) REVERT: C 152 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7462 (mm) REVERT: D 143 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6591 (tt0) REVERT: D 147 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6333 (mm) REVERT: D 330 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8730 (mp) REVERT: D 489 ASP cc_start: 0.7893 (m-30) cc_final: 0.7366 (m-30) REVERT: E 147 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6491 (mm) REVERT: E 152 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7400 (mm) REVERT: E 656 ILE cc_start: 0.7541 (mt) cc_final: 0.7310 (tt) REVERT: F 147 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6227 (mm) REVERT: F 330 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8717 (mp) REVERT: F 489 ASP cc_start: 0.7885 (m-30) cc_final: 0.7366 (m-30) REVERT: F 642 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: G 147 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6449 (mm) REVERT: H 330 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8737 (mp) REVERT: H 399 GLU cc_start: 0.7336 (tt0) cc_final: 0.6724 (tt0) REVERT: H 642 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7464 (pt0) outliers start: 91 outliers final: 44 residues processed: 303 average time/residue: 0.4402 time to fit residues: 217.9222 Evaluate side-chains 279 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 219 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 642 GLU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 LEU Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 618 VAL Chi-restraints excluded: chain H residue 642 GLU Chi-restraints excluded: chain H residue 645 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 305 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 233 optimal weight: 0.9980 chunk 416 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33659 Z= 0.189 Angle : 0.574 12.706 45418 Z= 0.269 Chirality : 0.038 0.207 5299 Planarity : 0.003 0.042 5862 Dihedral : 4.190 15.095 4710 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.17 % Allowed : 18.74 % Favored : 79.09 % 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: -0.07 (0.13), residues: 4212 helix: 0.77 (0.10), residues: 2934 sheet: -1.06 (0.38), residues: 104 loop : -1.98 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 253 HIS 0.002 0.000 HIS G 236 PHE 0.024 0.001 PHE C 617 TYR 0.008 0.001 TYR B 687 ARG 0.001 0.000 ARG E 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 224 time to evaluate : 3.471 Fit side-chains REVERT: A 147 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6553 (mm) REVERT: A 152 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7301 (mm) REVERT: B 330 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8726 (mp) REVERT: B 399 GLU cc_start: 0.8063 (mp0) cc_final: 0.7494 (tt0) REVERT: B 489 ASP cc_start: 0.7906 (m-30) cc_final: 0.7461 (m-30) REVERT: C 147 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6511 (mm) REVERT: C 152 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7215 (mm) REVERT: D 143 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: D 147 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6332 (mm) REVERT: D 330 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8729 (mp) REVERT: D 489 ASP cc_start: 0.7882 (m-30) cc_final: 0.7410 (m-30) REVERT: E 147 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6528 (mm) REVERT: E 152 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7178 (mm) REVERT: E 656 ILE cc_start: 0.7504 (mt) cc_final: 0.7283 (tt) REVERT: F 147 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6231 (mm) REVERT: F 330 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8718 (mp) REVERT: F 489 ASP cc_start: 0.7867 (m-30) cc_final: 0.7425 (m-30) REVERT: G 147 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6158 (mm) REVERT: H 330 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8722 (mp) REVERT: H 399 GLU cc_start: 0.7320 (tt0) cc_final: 0.6701 (tt0) REVERT: H 489 ASP cc_start: 0.7902 (m-30) cc_final: 0.7456 (m-30) REVERT: H 642 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7459 (pt0) outliers start: 73 outliers final: 44 residues processed: 279 average time/residue: 0.4415 time to fit residues: 202.0252 Evaluate side-chains 272 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 213 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain H residue 642 GLU Chi-restraints excluded: chain H residue 645 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 1.9990 chunk 166 optimal weight: 40.0000 chunk 248 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 chunk 81 optimal weight: 0.0770 chunk 80 optimal weight: 5.9990 chunk 264 optimal weight: 30.0000 chunk 283 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 327 optimal weight: 10.0000 overall best weight: 1.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33659 Z= 0.144 Angle : 0.554 12.558 45418 Z= 0.256 Chirality : 0.037 0.173 5299 Planarity : 0.003 0.049 5862 Dihedral : 3.954 14.239 4710 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.35 % Allowed : 18.89 % Favored : 78.76 % 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: 0.28 (0.14), residues: 4212 helix: 1.02 (0.10), residues: 2942 sheet: -0.49 (0.42), residues: 104 loop : -1.87 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 490 HIS 0.002 0.000 HIS G 236 PHE 0.023 0.001 PHE E 617 TYR 0.006 0.001 TYR B 687 ARG 0.001 0.000 ARG E 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 229 time to evaluate : 4.210 Fit side-chains REVERT: A 147 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6516 (mm) REVERT: A 152 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7238 (mm) REVERT: B 330 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8698 (mp) REVERT: B 399 GLU cc_start: 0.8023 (mp0) cc_final: 0.7459 (tt0) REVERT: B 489 ASP cc_start: 0.7868 (m-30) cc_final: 0.7523 (m-30) REVERT: C 147 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6461 (mm) REVERT: C 152 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7163 (mm) REVERT: D 143 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6513 (tt0) REVERT: D 147 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6246 (mm) REVERT: D 330 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8709 (mp) REVERT: D 489 ASP cc_start: 0.7902 (m-30) cc_final: 0.7590 (m-30) REVERT: E 147 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6440 (mm) REVERT: E 152 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7154 (mm) REVERT: E 656 ILE cc_start: 0.7563 (mt) cc_final: 0.7348 (tt) REVERT: F 147 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6246 (mm) REVERT: F 330 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8677 (mp) REVERT: F 489 ASP cc_start: 0.7862 (m-30) cc_final: 0.7513 (m-30) REVERT: F 642 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7270 (pt0) REVERT: G 147 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6182 (mm) REVERT: H 330 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8678 (mp) REVERT: H 399 GLU cc_start: 0.7252 (tt0) cc_final: 0.6627 (tt0) REVERT: H 489 ASP cc_start: 0.7885 (m-30) cc_final: 0.7543 (m-30) outliers start: 79 outliers final: 42 residues processed: 292 average time/residue: 0.4424 time to fit residues: 212.6445 Evaluate side-chains 277 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 220 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 642 GLU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Chi-restraints excluded: chain H residue 621 LEU Chi-restraints excluded: chain H residue 656 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 70.0000 chunk 398 optimal weight: 8.9990 chunk 363 optimal weight: 0.7980 chunk 388 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 350 optimal weight: 8.9990 chunk 366 optimal weight: 6.9990 chunk 386 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33659 Z= 0.273 Angle : 0.614 13.133 45418 Z= 0.286 Chirality : 0.040 0.179 5299 Planarity : 0.004 0.047 5862 Dihedral : 4.222 15.433 4710 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.32 % Allowed : 19.54 % Favored : 78.14 % 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: 0.09 (0.13), residues: 4212 helix: 0.87 (0.10), residues: 2950 sheet: -0.62 (0.42), residues: 104 loop : -1.93 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 638 HIS 0.003 0.001 HIS G 236 PHE 0.021 0.001 PHE E 617 TYR 0.009 0.001 TYR B 687 ARG 0.002 0.000 ARG F 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 220 time to evaluate : 3.417 Fit side-chains REVERT: A 147 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6577 (mm) REVERT: A 152 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7488 (mm) REVERT: B 330 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8757 (mp) REVERT: B 399 GLU cc_start: 0.8024 (mp0) cc_final: 0.7445 (tt0) REVERT: B 489 ASP cc_start: 0.7890 (m-30) cc_final: 0.7373 (m-30) REVERT: C 147 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6533 (mm) REVERT: C 152 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7395 (mm) REVERT: D 143 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6535 (tt0) REVERT: D 147 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6390 (mm) REVERT: D 330 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8740 (mp) REVERT: D 489 ASP cc_start: 0.7873 (m-30) cc_final: 0.7402 (m-30) REVERT: E 147 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6553 (mm) REVERT: E 152 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7320 (mm) REVERT: E 656 ILE cc_start: 0.7520 (mt) cc_final: 0.7277 (tt) REVERT: F 147 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6383 (mm) REVERT: F 330 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8724 (mp) REVERT: F 489 ASP cc_start: 0.7848 (m-30) cc_final: 0.7306 (m-30) REVERT: F 642 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: G 147 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6391 (mm) REVERT: H 330 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8752 (mp) REVERT: H 399 GLU cc_start: 0.7284 (tt0) cc_final: 0.6669 (tt0) REVERT: H 489 ASP cc_start: 0.7886 (m-30) cc_final: 0.7385 (m-30) outliers start: 78 outliers final: 45 residues processed: 284 average time/residue: 0.4341 time to fit residues: 202.1856 Evaluate side-chains 277 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 217 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 383 ASN Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 642 GLU Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 383 ASN Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Chi-restraints excluded: chain H residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 0.6980 chunk 410 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 285 optimal weight: 7.9990 chunk 430 optimal weight: 3.9990 chunk 396 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 35 optimal weight: 0.0470 chunk 264 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33659 Z= 0.188 Angle : 0.584 12.977 45418 Z= 0.269 Chirality : 0.038 0.175 5299 Planarity : 0.003 0.046 5862 Dihedral : 4.092 14.753 4710 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.90 % Allowed : 20.05 % Favored : 78.05 % 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: 0.26 (0.13), residues: 4212 helix: 1.07 (0.10), residues: 2926 sheet: -0.74 (0.42), residues: 152 loop : -2.05 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 214 HIS 0.002 0.000 HIS G 236 PHE 0.021 0.001 PHE E 617 TYR 0.008 0.001 TYR B 687 ARG 0.002 0.000 ARG F 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 223 time to evaluate : 3.736 Fit side-chains REVERT: A 147 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6562 (mm) REVERT: A 152 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7412 (mm) REVERT: A 514 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8944 (mt) REVERT: B 330 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8730 (mp) REVERT: B 399 GLU cc_start: 0.8031 (mp0) cc_final: 0.7434 (tt0) REVERT: B 489 ASP cc_start: 0.7910 (m-30) cc_final: 0.7476 (m-30) REVERT: C 147 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6555 (mm) REVERT: C 152 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7191 (mm) REVERT: D 143 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6518 (tt0) REVERT: D 147 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6400 (mm) REVERT: D 330 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8740 (mp) REVERT: D 489 ASP cc_start: 0.7895 (m-30) cc_final: 0.7454 (m-30) REVERT: E 147 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6538 (mm) REVERT: E 152 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7158 (mm) REVERT: F 147 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6263 (mm) REVERT: F 330 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8724 (mp) REVERT: F 489 ASP cc_start: 0.7889 (m-30) cc_final: 0.7460 (m-30) REVERT: F 642 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7351 (pt0) REVERT: G 147 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6372 (mm) REVERT: H 330 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8748 (mp) REVERT: H 399 GLU cc_start: 0.7257 (tt0) cc_final: 0.6647 (tt0) REVERT: H 489 ASP cc_start: 0.7867 (m-30) cc_final: 0.7495 (m-30) outliers start: 64 outliers final: 44 residues processed: 274 average time/residue: 0.4513 time to fit residues: 201.6151 Evaluate side-chains 278 residues out of total 3608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 218 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 593 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 621 LEU Chi-restraints excluded: chain F residue 642 GLU Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 383 ASN Chi-restraints excluded: chain G residue 593 ILE Chi-restraints excluded: chain G residue 645 THR Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 618 VAL Chi-restraints excluded: chain H residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 20.0000 chunk 365 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 chunk 50 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 343 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 352 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.164388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109724 restraints weight = 45655.889| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.83 r_work: 0.3083 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33659 Z= 0.178 Angle : 0.579 13.187 45418 Z= 0.266 Chirality : 0.038 0.173 5299 Planarity : 0.004 0.057 5862 Dihedral : 4.026 14.531 4710 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.96 % Allowed : 20.02 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.14), residues: 4212 helix: 1.12 (0.10), residues: 2942 sheet: -0.63 (0.42), residues: 152 loop : -1.97 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 214 HIS 0.002 0.000 HIS G 236 PHE 0.020 0.001 PHE C 617 TYR 0.007 0.001 TYR D 687 ARG 0.007 0.000 ARG A 543 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6536.90 seconds wall clock time: 119 minutes 25.07 seconds (7165.07 seconds total)